Added new modules, but build does not yet support them.

Modules/DCIP/examples/DCIPElectrode.cpp

@@ -0,0 +1,116 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      11/10/2014 12:31:01 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#include "DCIPElectrode.h"
+#include "DCSurvey.h"
+
+using namespace Lemma;
+
+int main() {
+
+
+    //DCIPElectrode* Electrode1 = DCIPElectrode::New();
+    DCIPElectrode* Electrode2 = DCIPElectrode::New();
+    DCIPElectrode* Electrode3 = DCIPElectrode::New();
+    DCIPElectrode* Electrode4 = DCIPElectrode::New();
+    DCIPElectrode* Electrode5 = DCIPElectrode::New();
+    DCIPElectrode* Electrode6 = DCIPElectrode::New();
+    DCIPElectrode* Electrode7 = DCIPElectrode::New();
+    DCIPElectrode* Electrode8 = DCIPElectrode::New();
+    DCIPElectrode* Electrode9 = DCIPElectrode::New();
+
+        //Electrode1->SetLocation( Vector3r( 23.23, 18.1, -45 )  );
+        Electrode2->SetLocation( Vector3r( 13.23, 18.1, -25 ) );
+        Electrode3->SetLocation( Vector3r( 13.23, 18.1, -25 ) );
+        Electrode4->SetLocation( Vector3r( 13.23, 18.1, -25 ) );
+        Electrode4->SetLocation( Vector3r( 13.23, 18.1, -25 ) );
+        Electrode5->SetLocation( Vector3r( 13.23, 18.1, -25 ) );
+        Electrode6->SetLocation( Vector3r( 13.23, 18.1, -25 ) );
+        Electrode7->SetLocation( Vector3r( 13.23, 18.1, -25 ) );
+        Electrode8->SetLocation( Vector3r( 13.23, 18.1, -25 ) );
+        Electrode9->SetLocation( Vector3r( 13.23, 18.1, -25 ) );
+
+//:        std::cout << *Electrode1 << std::endl;
+//     std::ofstream ofstr("DCIPElectrode.yaml");
+//         ofstr << *Electrode1;
+//         ofstr.close();
+
+    /*
+    //std::ifstream ifstr("DCIPElectrode.yaml");
+    std::ifstream ifstr("test.yaml");
+    YAML::Node node = YAML::Load(ifstr);
+    DCIPElectrode* Ex = DCIPElectrode::DeSerialize(node);
+    std::cout << *Ex << std::endl;
+    */
+    //exit(1);
+
+    //std::cout << *Electrode << std::endl;
+    //std::cout << *Electrode2 << std::endl;
+
+    // Set up a Survey
+    DCSurvey* Survey = DCSurvey::New();
+        // Instead we should just put location in, and then survey acts as factory?
+        DCIPElectrode* Electrode1 = Survey->PoundElectrode( Vector3r( 13.23, 18.1, -25 ), "L0-E0" );
+        Survey->PoundElectrode( Electrode2 , "L0-E1" );
+        Survey->PoundElectrode( Electrode3 , "L0-E2" );
+        Survey->PoundElectrode( Electrode4 , "L0-E3" );
+        Survey->PoundElectrode( Electrode5 , "L0-E4" );
+        Survey->PoundElectrode( Electrode6 , "L0-E5" );
+        Survey->PoundElectrode( Electrode7 , "L0-E6" );
+        Survey->PoundElectrode( Electrode8 , "L0-E7" );
+        Survey->PoundElectrode( Electrode9 , "L0-E8" );
+
+        int J0 = Survey->AddInjection( Electrode1, Electrode2, 1.0 );
+            Survey->AddMeasurement(J0, Electrode3, Electrode4 );
+            Survey->AddMeasurement(J0, Electrode5, Electrode6 );
+            Survey->AddMeasurement(J0, Electrode6, Electrode7 );
+            Survey->AddMeasurement(J0, "L0-E7", "L0-E8" );
+
+        int J1 = Survey->AddInjection( Electrode2, Electrode3, 1.0 );
+            Survey->AddMeasurement(J1, Electrode3, Electrode4 );
+            Survey->AddMeasurement(J1, Electrode5, Electrode6 );
+            Survey->AddMeasurement(J1, Electrode6, Electrode7 );
+
+        int J2 = Survey->AddInjection( Electrode3, Electrode4, 1.0 );
+            Survey->AddMeasurement(J2, Electrode3, Electrode4 );
+            Survey->AddMeasurement(J2, Electrode5, Electrode6 );
+            Survey->AddMeasurement(J2, Electrode6, Electrode7 );
+
+        //Survey->AddMeasurement(L1, L2)
+        std::cout << *Survey << std::endl;
+
+        std::ofstream outstr("DC.yaml");
+            outstr << *Survey << std::endl;
+            outstr.close();
+
+        Survey->Delete();
+
+        //TODO recheck DeSerialize make sure we are filling in all the Tag vectors
+
+        std::ifstream ifstr2("DC.yaml");
+        YAML::Node node2 = YAML::Load(ifstr2);
+        DCSurvey* Survey2 = DCSurvey::DeSerialize(node2);
+
+        std::cout << "==============================================================\n";
+        std::cout << *Survey2 << std::endl;
+
+    return(EXIT_SUCCESS);
+
+}
+

Modules/DCIP/include/DCIPElectrode.h

@@ -0,0 +1,127 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      11/10/2014 10:53:34 AM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+
+#ifndef  DCIPELECTRODE_INC
+#define  DCIPELECTRODE_INC
+
+#include "LemmaObject.h"
+
+namespace Lemma {
+
+    /**
+      \brief
+      \details
+     */
+    class DCIPElectrode : public LemmaObject {
+
+        friend std::ostream &operator<<(std::ostream &stream,
+                const DCIPElectrode &ob);
+
+        public:
+
+        // ====================  LIFECYCLE     =======================
+
+        /**
+         * @copybrief LemmaObject::New()
+         * @copydetails LemmaObject::New()
+         */
+        static DCIPElectrode* New();
+
+        /**
+         *  @copybrief   LemmaObject::Delete()
+         *  @copydetails LemmaObject::Delete()
+         */
+        void Delete();
+
+        // ====================  OPERATORS     =======================
+
+        // ====================  OPERATIONS    =======================
+
+        // ====================  ACCESS        =======================
+
+        /** Sets the physical location of the electrode
+         *  @param[in] loc is the location
+         */
+        void SetLocation(const Vector3r& loc);
+
+        /** Sets the tag (label) for the electrode
+         */
+        void SetLabel(const std::string& tag);
+
+        /** Sets the tag (label) for the electrode
+         */
+        std::string GetLabel( );
+
+        int GetNodeID() {return Node_ID;}
+        // ====================  INQUIRY       =======================
+
+#ifdef HAVE_YAMLCPP
+        /**
+         *  Uses YAML to serialize this object.
+         *  @return a YAML::Node
+         */
+        YAML::Node Serialize() const;
+
+        /**
+         *   Constructs an object from a YAML::Node.
+         */
+        static DCIPElectrode* DeSerialize(const YAML::Node& node);
+#endif
+
+        protected:
+
+        // ====================  LIFECYCLE     =======================
+
+        /** Default protected constructor, use New */
+        DCIPElectrode (const std::string& name);
+
+#ifdef HAVE_YAMLCPP
+        /** Protected DeDerializing constructor, use factory DeSerialize  method*/
+        DCIPElectrode (const YAML::Node& node);
+#endif
+
+        /** Default protected destructor, use Delete */
+        ~DCIPElectrode ();
+
+        /**
+         *  @copybrief   LemmaObject::Release()
+         *  @copydetails LemmaObject::Release()
+         */
+        void Release();
+
+        private:
+
+        // ====================  DATA MEMBERS  =========================
+
+        /** The location of the electrode */
+        Vector3r Location;
+
+        /** Local Node_ID on a mesh */
+        int Node_ID;
+
+        /** String label for the electrode */
+        std::string Label;
+
+    }; // -----  end of class  DCIPElectrode  -----
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef DCIPELECTRODE_INC  -----
+

Modules/DCIP/include/DCSurvey.h

@@ -0,0 +1,240 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      10/08/2014 01:51:50 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#ifndef  DCSURVEY
+#define  DCSURVEY
+
+#include "LemmaObject.h"
+#include "DCIPElectrode.h"
+
+#ifdef HAVE_YAMLCPP
+#include "yaml-cpp/yaml.h"
+#endif
+
+#ifdef LEMMAUSEVTK
+#include <vtkDataSet.h>
+#endif
+
+namespace Lemma {
+
+    #define EINFINITY -9999
+
+    /**
+      \brief   Describes a DC survey.
+      \details This class aims to encapulate any type of DC survey.
+     */
+    class DCSurvey : public LemmaObject {
+
+        friend std::ostream &operator<<(std::ostream &stream,
+                const DCSurvey &ob);
+
+        public:
+
+        // ====================  LIFECYCLE     =======================
+
+        /**
+         * @copybrief LemmaObject::New()
+         * @copydetails LemmaObject::New()
+         */
+        static DCSurvey* New();
+
+        /**
+         *  @copybrief   LemmaObject::Delete()
+         *  @copydetails LemmaObject::Delete()
+         */
+        void Delete();
+
+        // ====================  OPERATORS     =======================
+
+        // ====================  OPERATIONS    =======================
+
+        /**
+         *   Adds new electrode to the survey.
+         *   @param[in] Electrode `Pounds' a new Electrode into place.
+         *   @return integer index to this electrode.
+         *   @note Single electrodes cannot be pulled once they are pounded. The reason for this is that
+         *         every index then would become invalid. Furthurmore these are stored in a std::vector and
+         *         removing arbitrary items is inefficient.
+         *   @see PullElectrodes
+         *   @param[in] label is an optional tag for electrode.
+         *   @param[in] nodeID is the optional node ID on a mesh
+         */
+        int PoundElectrode( DCIPElectrode* Electrode, const std::string& label = "NULL", const int& nodeID=-1 );
+
+        /** Alternative Factory method of setting electrodes. IN this manner all memoy management
+         *  is handled by DCSurvey.
+         *  @note there is no logic preventing one from pounding coincident electrodes. Don't do it.
+         *  @note Single electrodes cannot be pulled once they are pounded. The reason for this is that
+         *         every index then would become invalid. Furthurmore these are stored in a std::vector and
+         *         removing arbitrary items is inefficient.
+         *  @see PullElectrodes
+         *  @param[in] loc is the location of the electrode.
+         *  @param[in] label is an optional label for electrode.
+         *  @param[in] nodeID is the optional node ID on a mesh
+         */
+        DCIPElectrode* PoundElectrode( const Vector3r& loc, const std::string& label = "NULL", const int& nodeID=-1  );
+
+#ifdef LEMMAUSEVTK
+        DCIPElectrode* PoundElectrode( const int& nodeID, vtkDataSet* Mesh, const std::string& label = "NULL" );
+#endif
+
+        /**
+         *  Pulls all electrodes and removes connections.
+         */
+        void PullElectrodes();
+
+        /**
+         *   Adds an injection point.
+         *   @param[in] A is the positive current electrode
+         *   @param[in] B is the negative current electrode
+         *   @param[in] J is the current intensity
+         *   @see AddInjection(const int& iA, const int& iB, const Real& J)
+         *   @see AddInjection(const int& iA, const Real& J)
+         *   @see AddInjection(DCIPElectrode* A, const Real& J)
+         */
+        int AddInjection( DCIPElectrode* A, DCIPElectrode* B, const Real& J);
+
+        /**
+         *   Adds an injection point.
+         *   @param[in] A is the positive current electrode.
+         *   @param[in] J is the current intensity.
+         *   B,  the negative current electrode is taken to be infinity
+         *   @see AddInjection(const int& iA, const int& iB, const Real& J)
+         *   @see AddInjection(const int& iA, const Real& J)
+         *   @see AddInjection(DCIPElectrode* A, DCIPElectrode* B, const Real& J)
+         */
+        int AddInjection( DCIPElectrode* A, const Real& J );
+
+        /**
+         *   Adds an injection point.
+         *   @param[in] A is the positive current electrode index
+         *   @param[in] B is the negative current electrode index
+         *   @param[in] J is the current intensity
+         *   @see AddInjection(DCIPElectrode* A, DCIPElectrode* B, const Real& J)
+         *   @see AddInjection(DCIPElectrode* A, const Real& J)
+         *   @see AddInjection(const int& iA, const Real& J)
+         */
+        int AddInjection( const int& iA, const int& iB, const Real& J );
+
+        /**
+         *   Adds an injection point with the negative electrode at infinity.
+         *   @param[in] A is the positive current electrode index
+         *   @param[in] J is the current intensity
+         *   @see AddInjection(DCIPElectrode* A, DCIPElectrode* B, const Real& J)
+         *   @see AddInjection(DCIPElectrode* A, const Real& J)
+         *   @see AddInjection(const int& iA, const int& iB, const Real& J)
+         */
+        int AddInjection( const int& iA, const Real& J );
+
+        /** Adds a potential measurement via the electrode pair comparison \f$ M - N \f$.
+         *   @param[in] M is a pointer to the `positive' electrode
+         *   @param[in] N is a pointer to the `negative' electrode
+         *   @param[in] iJ is the current injection index to associate with this measurement
+         */
+        void AddMeasurement( const int& iJ, DCIPElectrode* M, DCIPElectrode* N );
+
+        /** Adds a potential measurement via the electrode pair comparison \f$ M - N \f$.
+         *   @param[in] M is the `positive' electrode string label name
+         *   @param[in] N is the `negative' electrode string label name
+         *   @param[in] iJ is the current injection index to associate with this measurement
+         *   @see AddMeasurement( const int& iJ, DCIPElectrode* M, DCIPElectrode* N )
+         */
+        void AddMeasurement( const int& ij, const std::string& M, const std::string& N);
+
+        /**
+         *  Used to probe for the index and current of an injection
+         *  @param[in] ij is the current injection indes
+         *  @param[out] ii is the node index
+         *  @param[out] jj is the current
+         */
+        void GetA( const int& ij, int& ii, Real& jj );
+
+        /**
+         *  Used to probe for the index and current of an injection
+         *  @param[in] ij is the current injection indes
+         *  @param[out] ii is the node index
+         *  @param[out] jj is the current
+         */
+        void GetB( const int& ij, int& ii, Real& jj );
+
+
+        // ====================  ACCESS        =======================
+
+        // ====================  INQUIRY       =======================
+
+        #ifdef HAVE_YAMLCPP
+        YAML::Node Serialize() const;
+        static DCSurvey* DeSerialize(const YAML::Node& node);
+        #endif
+
+        protected:
+
+        // ====================  LIFECYCLE     =======================
+
+        /** Default protected constructor, use New */
+        DCSurvey (const std::string& name);
+
+        #ifdef HAVE_YAMLCPP
+        /** Default protected constructor, use New */
+        DCSurvey (const YAML::Node& node);
+        #endif
+
+        /** Default protected destructor, use Delete */
+        ~DCSurvey ();
+
+        /**
+         *  @copybrief   LemmaObject::Release()
+         *  @copydetails LemmaObject::Release()
+         */
+        void Release();
+
+        private:
+
+        // ====================  DATA MEMBERS  =========================
+
+        /** The electrodes */
+        std::vector<DCIPElectrode*>                Electrodes;
+
+        /** Tags for the electrodes, lines etc. Ordered with Electrodes std::vector */
+        std::vector<std::string>                   OrderedElectrodeLabels;
+
+        /** Map of tags for the electrodes, lines etc. */
+        std::map<std::string, std::pair<DCIPElectrode*, int> >      ElectrodeLabelMap;
+
+        /** The A Injection electrodes */
+        std::vector<int>     A_Electrodes;
+
+        /** The A Injection electrodes */
+        std::vector<int>     B_Electrodes;
+
+        /** The A Injection electrodes */
+        std::vector<Real>    J_Electrodes;
+
+        /** First Potential electrodes */
+        std::vector< std::vector<int> > M_Electrodes;
+
+        /** Second Potential electrodes */
+        std::vector< std::vector<int> > N_Electrodes;
+
+    }; // -----  end of class  DCSurvey  -----
+
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef DCSURVEY  -----

Modules/DCIP/src/DCIPElectrode.cpp

@@ -0,0 +1,165 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      11/10/2014 10:53:53 AM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#include "DCIPElectrode.h"
+
+namespace Lemma {
+
+
+
+    // ====================  FRIEND METHODS  =====================
+#ifdef HAVE_YAMLCPP
+    std::ostream &operator << (std::ostream &stream, const DCIPElectrode &ob) {
+        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulate thingy
+        return stream;
+    }
+#else
+    std::ostream &operator<<(std::ostream &stream, const DCIPElectrode& ob) {
+        stream << *(LemmaObject*)(&ob);
+        return stream;
+    }
+#endif
+
+    // ====================  LIFECYCLE     =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCIPElectrode
+    //      Method:  DCIPElectrode
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    DCIPElectrode::DCIPElectrode (const std::string& name) : LemmaObject(name), Node_ID(-1), Label(std::string("None")) {
+
+    }  // -----  end of method DCIPElectrode::DCIPElectrode  (constructor)  -----
+
+#ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCIPElectrode
+    //      Method:  DCIPElectrode
+    // Description:  DeSerializing constructor (protected)
+    //--------------------------------------------------------------------------------------
+    DCIPElectrode::DCIPElectrode (const YAML::Node& node) : LemmaObject(node) {
+        if (node.Tag() != this->Name) {
+            throw std::runtime_error("In DCIPElectrode(node), node is of wrong type");
+        }
+        this->Location = node["Location"].as<Vector3r>();
+        this->Node_ID = node["Node_ID"].as<int>();
+        this->Label = node["Label"].as<std::string>();
+    }  // -----  end of method DCIPElectrode::DCIPElectrode  (constructor)  -----
+#endif
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCIPElectrode
+    //      Method:  New()
+    // Description:  public constructor
+    //--------------------------------------------------------------------------------------
+    DCIPElectrode* DCIPElectrode::New() {
+        DCIPElectrode*  Obj = new DCIPElectrode("DCIPElectrode");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCIPElectrode
+    //      Method:  ~DCIPElectrode
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    DCIPElectrode::~DCIPElectrode () {
+
+    }  // -----  end of method DCIPElectrode::~DCIPElectrode  (destructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCIPElectrode
+    //      Method:  Delete
+    // Description:  public destructor
+    //--------------------------------------------------------------------------------------
+    void DCIPElectrode::Delete() {
+        this->DetachFrom(this);
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCIPElectrode
+    //      Method:  Release
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    void DCIPElectrode::Release() {
+        delete this;
+    }
+
+
+#ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCIPElectrode
+    //      Method:  Serialize
+    //--------------------------------------------------------------------------------------
+    YAML::Node  DCIPElectrode::Serialize (  ) const {
+        YAML::Node node = LemmaObject::Serialize();
+        node.SetTag( this->Name );
+        // FILL IN CLASS SPECIFICS HERE
+        node["Location"] = Location;
+        node["Node_ID"] = Node_ID;
+        node["Label"] = Label;
+        return node;
+    }		// -----  end of method DCIPElectrode::Serialize  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCIPElectrode
+    //      Method:  DeSerialize
+    //--------------------------------------------------------------------------------------
+    DCIPElectrode* DCIPElectrode::DeSerialize ( const YAML::Node& node  ) {
+        DCIPElectrode* Object = new DCIPElectrode(node);
+        Object->AttachTo(Object);
+        DESERIALIZECHECK( node, Object )
+        return Object ;
+    }		// -----  end of method DCIPElectrode::DeSerialize  -----
+#endif
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCIPElectrode
+    //      Method:  SetLocation
+    //--------------------------------------------------------------------------------------
+    void DCIPElectrode::SetLocation ( const Vector3r& loc ) {
+        Location = loc;
+        return ;
+    }		// -----  end of method DCIPElectrode::SetLocation  -----
+
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCIPElectrode
+    //      Method:  SetTag
+    //--------------------------------------------------------------------------------------
+    void DCIPElectrode::SetLabel ( const std::string& inLabel  ) {
+        Label = inLabel;
+        return ;
+    }		// -----  end of method DCIPElectrode::SetTag  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCIPElectrode
+    //      Method:  get_Label
+    //--------------------------------------------------------------------------------------
+    std::string DCIPElectrode::GetLabel (  ) {
+        return Label;
+    }		// -----  end of method DCIPElectrode::get_Label  -----
+
+
+}		// -----  end of Lemma  name  -----
+

Modules/DCIP/src/DCSurvey.cpp

@@ -0,0 +1,377 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      10/08/2014 01:52:04 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#include	"DCSurvey.h"
+
+namespace Lemma {
+
+
+    // ====================  FRIEND METHODS  =====================
+
+    #ifdef HAVE_YAMLCPP
+    std::ostream &operator << (std::ostream &stream, const DCSurvey &ob) {
+        stream << ob.Serialize()  << "\n---\n"; // End of doc --- a direct stream should encapsulate object
+        return stream;
+    }
+    #else
+    std::ostream &operator<<(std::ostream &stream, const DCSurvey &ob) {
+        stream << *(LemmaObject*)(&ob);
+        return stream;
+    }
+    #endif
+
+    // ====================  LIFECYCLE     =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCSurvey
+    //      Method:  DCSurvey
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    DCSurvey::DCSurvey (const std::string& name) : LemmaObject(name) {
+
+    }  // -----  end of method DCSurvey::DCSurvey  (constructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCSurvey
+    //      Method:  DCSurvey
+    // Description:  DeSerializing constructor (protected)
+    //--------------------------------------------------------------------------------------
+    #ifdef HAVE_YAMLCPP
+    DCSurvey::DCSurvey (const YAML::Node& node) : LemmaObject(node) {
+
+        if (node.Tag() != "DCSurvey") {
+            throw std::runtime_error("DCSurvey->DeSerialize cannot deserialize non-DCSurvey");
+        }
+
+        std::map<YAML::Node, int>  eMap;
+        for(YAML::const_iterator it=node["Electrodes"].begin(); it!=node["Electrodes"].end(); ++it) {
+            std::string e = it->first.as<std::string>();
+            Electrodes.push_back( DCIPElectrode::DeSerialize( node["Electrodes"][e] ) );
+            Electrodes[Electrodes.size()-1]->AttachTo(this);
+            eMap[ node["Electrodes"][Electrodes.size()-1] ] = Electrodes.size() -1 ;
+            OrderedElectrodeLabels.push_back(e);
+            ElectrodeLabelMap[e] = std::pair<DCIPElectrode*, int>(Electrodes[Electrodes.size()-1], Electrodes.size()-1);
+        }
+
+        //std::cout << "J-0\n" << node["Injections"]["J-0"] << std::endl;
+        int ij = 0 ;
+        for(YAML::const_iterator it=node["Injections"].begin(); it!=node["Injections"].end(); ++it) {
+
+            //std::cout << "it->first" << it->first << std::endl;
+
+            A_Electrodes.push_back( ElectrodeLabelMap[ it->second["A"]["Label"].as<std::string>() ].second );
+            B_Electrodes.push_back( ElectrodeLabelMap[ it->second["B"]["Label"].as<std::string>() ].second );
+            J_Electrodes.push_back( it->second["J"].as<Real>() );
+            //std::string Jstr = it->first.as<std::string>(); // J-1
+
+            M_Electrodes.push_back( std::vector<int>() );
+            N_Electrodes.push_back( std::vector<int>() );
+
+            for (int ii=0; ii<it->second["Measurements"]["Number"].as<int>(); ++ii) {
+                std::string Mstr = std::string("V-") + to_string(ii);
+                //std::cout << "measurements" << it->second["Measurements"][Mstr]["M"]["Label"] << std::endl;
+                M_Electrodes[ij].push_back( ElectrodeLabelMap[ it->second["Measurements"][Mstr]["M"]["Label"].as<std::string>() ].second );
+                N_Electrodes[ij].push_back( ElectrodeLabelMap[ it->second["Measurements"][Mstr]["N"]["Label"].as<std::string>() ].second );
+            }
+            ++ ij;
+        }
+
+    }  // -----  end of method DCSurvey::DCSurvey  (constructor)  -----
+    #endif
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCSurvey
+    //      Method:  New()
+    // Description:  public constructor
+    //--------------------------------------------------------------------------------------
+    DCSurvey* DCSurvey::New() {
+        DCSurvey*  Obj = new DCSurvey("DCSurvey");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCSurvey
+    //      Method:  ~DCSurvey
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    DCSurvey::~DCSurvey () {
+
+    }  // -----  end of method DCSurvey::~DCSurvey  (destructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCSurvey
+    //      Method:  Delete
+    // Description:  public destructor
+    //--------------------------------------------------------------------------------------
+    void DCSurvey::Delete() {
+        this->DetachFrom(this);
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCSurvey
+    //      Method:  Release
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    void DCSurvey::Release() {
+        this->PullElectrodes();
+        delete this;
+    }
+
+    #ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCSurvey
+    //      Method:  Serialize
+    //--------------------------------------------------------------------------------------
+    YAML::Node  DCSurvey::Serialize (  ) const {
+        YAML::Node node = LemmaObject::Serialize();
+        node.SetTag( this->Name );
+        node["NumberOfElectrodes"] = Electrodes.size();
+
+        // All the electrodes
+        for (std::map<std::string, std::pair<DCIPElectrode*, int> >::const_iterator it  = ElectrodeLabelMap.begin();
+                                                                                    it != ElectrodeLabelMap.end(); ++it) {
+            node["Electrodes"][ it->first ] = it->second.first->Serialize();
+        }
+
+        // Injections and Measurements
+        for (unsigned int ic=0; ic<A_Electrodes.size(); ++ic) {
+            std::string strLab = std::string("J-") + to_string(ic);
+            node["Injections"][strLab]["A"] = node["Electrodes"][ OrderedElectrodeLabels[ A_Electrodes[ic] ] ];
+            node["Injections"][strLab]["B"] = node["Electrodes"][ OrderedElectrodeLabels[ B_Electrodes[ic] ] ];
+            node["Injections"][strLab]["J"] = J_Electrodes[ic];
+            node["Injections"][strLab]["Measurements"]["Number"] = M_Electrodes[ic].size();
+            for (unsigned int iv=0; iv<M_Electrodes[ic].size(); ++iv) {
+                node["Injections"][strLab]["Measurements"][std::string("V-") + to_string(iv)]["M"] =
+                    node["Electrodes"][ OrderedElectrodeLabels[M_Electrodes[ic][iv]] ];
+                node["Injections"][strLab]["Measurements"][std::string("V-") + to_string(iv)]["N"] =
+                    node["Electrodes"][ OrderedElectrodeLabels[N_Electrodes[ic][iv]] ];
+            }
+        }
+
+        return node;
+    }		// -----  end of method DCSurvey::Serialize  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCSurvey
+    //      Method:  DeSerialize
+    //--------------------------------------------------------------------------------------
+    DCSurvey* DCSurvey::DeSerialize ( const YAML::Node& node  ) {
+        DCSurvey* Object = new DCSurvey(node);
+        Object->AttachTo(Object);
+        DESERIALIZECHECK( node, Object )
+        return Object ;
+    }		// -----  end of method DCSurvey::DeSerialize  -----
+    #endif
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCSurvey
+    //      Method:  PoundElectrode
+    //--------------------------------------------------------------------------------------
+    int DCSurvey::PoundElectrode ( DCIPElectrode* Electrode, const std::string& tag, const int&nodeID ) {
+        Electrodes.push_back(Electrode);
+        if (tag != "NULL") {
+            OrderedElectrodeLabels.push_back(tag);
+            //ElectrodeTagMap[tag] = Electrode;
+            ElectrodeLabelMap[tag] = std::pair<DCIPElectrode*, int> (Electrode, Electrodes.size()-1);
+            Electrode->SetLabel(tag);
+        } else {
+            OrderedElectrodeLabels.push_back( std::string("E") + to_string(Electrodes.size()-1) );
+            //ElectrodeTagMap[std::string("E") + to_string(Electrodes.size()-1)] = Electrode;
+            ElectrodeLabelMap[std::string("E") + to_string(Electrodes.size()-1)] =
+                std::pair<DCIPElectrode*, int>(Electrode, Electrodes.size()-1);
+            Electrode->SetLabel( std::string("E") + to_string(Electrodes.size()-1) );
+        }
+        Electrode->AttachTo(this);
+        return  static_cast<int>( Electrodes.size() ) ;
+    }		// -----  end of method DCSurvey::PoundElectrode  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCSurvey
+    //      Method:  PoundElectrode
+    //--------------------------------------------------------------------------------------
+    DCIPElectrode* DCSurvey::PoundElectrode ( const Vector3r& loc, const std::string& tag, const int& nodeID ) {
+        DCIPElectrode* Electrode = DCIPElectrode::New();
+            Electrode->SetLocation( loc );
+        Electrodes.push_back(Electrode);
+        if (tag != "NULL") {
+            OrderedElectrodeLabels.push_back(tag);
+            ElectrodeLabelMap[tag] = std::pair<DCIPElectrode*, int> (Electrode, Electrodes.size()-1);
+            Electrode->SetLabel(tag);
+        } else {
+            OrderedElectrodeLabels.push_back( std::string("E") + to_string(Electrodes.size()-1) );
+            ElectrodeLabelMap[std::string("E") + to_string(Electrodes.size()-1)] =
+                std::pair<DCIPElectrode*, int>(Electrode, Electrodes.size()-1);
+            Electrode->SetLabel( std::string("E") + to_string(Electrodes.size()-1) );
+        }
+        Electrode->AttachTo(this);
+        return  Electrode;
+    }		// -----  end of method DCSurvey::PoundElectrode  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCSurvey
+    //      Method:  PoundElectrode
+    //--------------------------------------------------------------------------------------
+#ifdef LEMMAUSEVTK
+    DCIPElectrode* DCSurvey::PoundElectrode( const int& nodeID, vtkDataSet* Mesh, const std::string& tag ) {
+        DCIPElectrode* Electrode = DCIPElectrode::New();
+        double* loc = Mesh->GetPoint(nodeID);
+        Electrode->SetLocation( Vector3r(loc[0], loc[1], loc[2]) );
+        Electrodes.push_back(Electrode);
+        if (tag != "NULL") {
+            OrderedElectrodeLabels.push_back(tag);
+            ElectrodeLabelMap[tag] = std::pair<DCIPElectrode*, int> (Electrode, Electrodes.size()-1);
+            Electrode->SetLabel(tag);
+        } else {
+            OrderedElectrodeLabels.push_back( std::string("E") + to_string(Electrodes.size()-1) );
+            ElectrodeLabelMap[std::string("E") + to_string(Electrodes.size()-1)] =
+                std::pair<DCIPElectrode*, int>(Electrode, Electrodes.size()-1);
+            Electrode->SetLabel( std::string("E") + to_string(Electrodes.size()-1) );
+        }
+        Electrode->AttachTo(this);
+        return Electrode;
+    }		// -----  end of method DCSurvey::PoundElectrode  -----
+#endif
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCSurvey
+    //      Method:  PullElectrodes
+    //--------------------------------------------------------------------------------------
+    void DCSurvey::PullElectrodes (  ) {
+        for (std::vector<DCIPElectrode*>::iterator it = Electrodes.begin() ; it != Electrodes.end(); ++it) {
+            (*it)->DetachFrom(this);
+        }
+        Electrodes.clear();
+        OrderedElectrodeLabels.clear();
+        ElectrodeLabelMap.clear();
+        A_Electrodes.clear();
+        B_Electrodes.clear();
+        M_Electrodes.clear();
+        N_Electrodes.clear();
+
+        return ;
+    }		// -----  end of method DCSurvey::PullElectrodes  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCSurvey
+    //      Method:  AddInjection
+    //--------------------------------------------------------------------------------------
+    int DCSurvey::AddInjection ( DCIPElectrode* A, DCIPElectrode* B, const Real& J ) {
+        bool fA = false;
+        bool fB = false;
+        for (unsigned int i=0; i<Electrodes.size(); ++i) {
+            if (Electrodes[i] == A) {
+                A_Electrodes.push_back(i);
+                M_Electrodes.push_back( std::vector<int>() );
+                N_Electrodes.push_back( std::vector<int>() );
+                fA = true;
+            }
+            if (Electrodes[i] == B) {
+                B_Electrodes.push_back(i);
+                fB = true;
+            }
+            if (fA == true && fB == true) break;
+        }
+        if (!fA) {
+            throw std::runtime_error( "Injection point A not found" );
+        }
+        if (!fB) {
+            throw std::runtime_error( "Injection point B not found" );
+        }
+        J_Electrodes.push_back(J);
+        return A_Electrodes.size()-1; // we want index
+    }		// -----  end of method DCSurvey::AddInjection  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCSurvey
+    //      Method:  AddMeasurement
+    //--------------------------------------------------------------------------------------
+    void DCSurvey::AddMeasurement ( const int& iJ, DCIPElectrode* M, DCIPElectrode* N  ) {
+        bool fM = false;
+        bool fN = false;
+        for (unsigned int i=0; i<Electrodes.size(); ++i) {
+            if (Electrodes[i] == M) {
+                M_Electrodes[iJ].push_back(i);
+                fM = true;
+            }
+            if (Electrodes[i] == N) {
+                N_Electrodes[iJ].push_back(i);
+                fN = true;
+            }
+            if (fM == true && fN == true) break;
+        }
+        if (!fM) {
+            throw std::runtime_error( "Injection point M not found" );
+        }
+        if (!fN) {
+            throw std::runtime_error( "Injection point N not found" );
+        }
+        return ;
+    }		// -----  end of method DCSurvey::AddMeasurement  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCSurvey
+    //      Method:  AddMeasurement
+    //--------------------------------------------------------------------------------------
+
+    void DCSurvey::AddMeasurement ( const int& iJ, const std::string& M, const std::string& N ) {
+
+        std::pair<DCIPElectrode*, int> Mp = ElectrodeLabelMap[M];
+        std::pair<DCIPElectrode*, int> Np = ElectrodeLabelMap[N];
+
+        if (Mp.first == NULL) {
+            throw std::runtime_error( "Injection point M not found" );
+        }
+        if (Np.first == NULL) {
+            throw std::runtime_error( "Injection point N not found" );
+        }
+
+        M_Electrodes[iJ].push_back( Mp.second );
+        N_Electrodes[iJ].push_back( Np.second );
+
+        return ;
+    }		// -----  end of method DCSurvey::AddMeasurement  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCSurvey
+    //      Method:  GetA
+    //--------------------------------------------------------------------------------------
+    void DCSurvey::GetA (const int& iA, int& iB, Real& J ) {
+        iB = Electrodes[A_Electrodes[iA]]->GetNodeID();
+        J = J_Electrodes[iA];
+        return ;
+    }		// -----  end of method DCSurvey::GetA  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  DCSurvey
+    //      Method:  GetB
+    //--------------------------------------------------------------------------------------
+    void DCSurvey::GetB (const int& iA, int& iB, Real& J ) {
+        iB = Electrodes[B_Electrodes[iA]]->GetNodeID();
+        J = -J_Electrodes[iA];
+        return ;
+    }		// -----  end of method DCSurvey::GetA  -----
+
+
+}		// -----  end of Lemma  name  -----
+

Modules/FDEM1D/include/FHTKey.h

@@ -0,0 +1,112 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      02/11/2014 03:33:08 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+
+#ifndef  FHTKEY_INC
+#define  FHTKEY_INC
+
+#include "hankeltransform.h"
+
+namespace Lemma {
+
+    /**
+      \brief   Impliments the fast Hankel transform as outlines by Key 2011
+      \details This filter uses 61, 121, or 201 filter points and supports both lagged and related
+                kernel arguments. This algorithm is a port of code carrying the following copyright and
+                restriction:
+                %------------------------------------------------------------------%
+                % Copyright (c) 2012 by the Society of Exploration Geophysicists.  %
+                % For more information, go to http://software.seg.org/2012/0003 .  %
+                % You must read and accept usage terms at:                         %
+                % http://software.seg.org/disclaimer.txt before use.               %
+                %------------------------------------------------------------------%
+     */
+    class FHTKey : public HankelTransform {
+
+        friend std::ostream &operator<<(std::ostream &stream,
+                const FHTKey &ob);
+
+        public:
+
+        // ====================  LIFECYCLE     =======================
+
+        /**
+         * @copybrief LemmaObject::New()
+         * @copydetails LemmaObject::New()
+         */
+        static FHTKey* New();
+
+        /**
+         *  @copybrief   LemmaObject::Delete()
+         *  @copydetails LemmaObject::Delete()
+         */
+        void Delete();
+
+        // ====================  OPERATORS     =======================
+
+        // ====================  OPERATIONS    =======================
+
+        Complex Zgauss(const int &ikk, const EMMODE &imode,
+                            const int &itype, const Real &rho,
+                            const Real &wavef, KernelEm1DBase *Kernel);
+
+        /// Computes related kernels, if applicable, otherwise this is
+        /// just a dummy function.
+        void ComputeRelated(const Real& rho, KernelEm1DBase* Kernel);
+
+        void ComputeRelated(const Real& rho, std::vector< KernelEm1DBase* > KernelVec);
+
+        void ComputeRelated(const Real& rho, KernelEM1DManager* KernelManager);
+
+        // ====================  ACCESS        =======================
+
+        // ====================  INQUIRY       =======================
+
+        protected:
+
+        // ====================  LIFECYCLE     =======================
+
+        /** Default protected constructor, use New */
+        FHTKey (const std::string& name);
+
+        /** Default protected destructor, use Delete */
+        ~FHTKey ();
+
+        /**
+         *  @copybrief   LemmaObject::Release()
+         *  @copydetails LemmaObject::Release()
+         */
+        void Release();
+
+        private:
+
+        // ====================  DATA MEMBERS  =========================
+
+        // Shared Filter Weights
+		static const Eigen::Matrix<Real, 201, 3>  WT201;
+
+        /// Holds answer, dimensions are NumConv, and NumberRelated.
+        Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic> Zans;
+
+    }; // -----  end of class  FHTKey  -----
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef FHTKEY_INC  -----
+

Modules/FDEM1D/include/FHTKey101.h

@@ -0,0 +1,112 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      02/11/2014 03:33:08 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+
+#ifndef  FHTKEY101_INC
+#define  FHTKEY101_INC
+
+#include "hankeltransform.h"
+
+namespace Lemma {
+
+    /**
+      \brief   Impliments the fast Hankel transform as outlines by Key 2011
+      \details This filter uses 51, 101, or 201 filter points and supports both lagged and related
+                kernel arguments. This algorithm is a port of code carrying the following copyright and
+                restriction:
+                %------------------------------------------------------------------%
+                % Copyright (c) 2012 by the Society of Exploration Geophysicists.  %
+                % For more information, go to http://software.seg.org/2012/0003 .  %
+                % You must read and accept usage terms at:                         %
+                % http://software.seg.org/disclaimer.txt before use.               %
+                %------------------------------------------------------------------%
+     */
+    class FHTKey101 : public HankelTransform {
+
+        friend std::ostream &operator<<(std::ostream &stream,
+                const FHTKey101 &ob);
+
+        public:
+
+        // ====================  LIFECYCLE     =======================
+
+        /**
+         * @copybrief LemmaObject::New()
+         * @copydetails LemmaObject::New()
+         */
+        static FHTKey101* New();
+
+        /**
+         *  @copybrief   LemmaObject::Delete()
+         *  @copydetails LemmaObject::Delete()
+         */
+        void Delete();
+
+        // ====================  OPERATORS     =======================
+
+        // ====================  OPERATIONS    =======================
+
+        Complex Zgauss(const int &ikk, const EMMODE &imode,
+                            const int &itype, const Real &rho,
+                            const Real &wavef, KernelEm1DBase *Kernel);
+
+        /// Computes related kernels, if applicable, otherwise this is
+        /// just a dummy function.
+        void ComputeRelated(const Real& rho, KernelEm1DBase* Kernel);
+
+        void ComputeRelated(const Real& rho, std::vector< KernelEm1DBase* > KernelVec);
+
+        void ComputeRelated(const Real& rho, KernelEM1DManager* KernelManager);
+
+        // ====================  ACCESS        =======================
+
+        // ====================  INQUIRY       =======================
+
+        protected:
+
+        // ====================  LIFECYCLE     =======================
+
+        /** Default protected constructor, use New */
+        FHTKey101 (const std::string& name);
+
+        /** Default protected destructor, use Delete */
+        ~FHTKey101 ();
+
+        /**
+         *  @copybrief   LemmaObject::Release()
+         *  @copydetails LemmaObject::Release()
+         */
+        void Release();
+
+        private:
+
+        // ====================  DATA MEMBERS  =========================
+
+        // Shared Filter Weights
+		static const Eigen::Matrix<Real, 101, 3>  WT101;
+
+        /// Holds answer, dimensions are NumConv, and NumberRelated.
+        Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic> Zans;
+
+    }; // -----  end of class  FHTKey101  -----
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef FHTKEY101_INC  -----
+

Modules/FDEM1D/include/FHTKey51.h

@@ -0,0 +1,112 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      02/11/2014 03:33:08 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+
+#ifndef  FHTKEY51_INC
+#define  FHTKEY51_INC
+
+#include "hankeltransform.h"
+
+namespace Lemma {
+
+    /**
+      \brief   Impliments the fast Hankel transform as outlines by Key 2011
+      \details This filter uses 51, 101, or 201 filter points and supports both lagged and related
+                kernel arguments. This algorithm is a port of code carrying the following copyright and
+                restriction:
+                %------------------------------------------------------------------%
+                % Copyright (c) 2012 by the Society of Exploration Geophysicists.  %
+                % For more information, go to http://software.seg.org/2012/0003 .  %
+                % You must read and accept usage terms at:                         %
+                % http://software.seg.org/disclaimer.txt before use.               %
+                %------------------------------------------------------------------%
+     */
+    class FHTKey51 : public HankelTransform {
+
+        friend std::ostream &operator<<(std::ostream &stream,
+                const FHTKey51 &ob);
+
+        public:
+
+        // ====================  LIFECYCLE     =======================
+
+        /**
+         * @copybrief LemmaObject::New()
+         * @copydetails LemmaObject::New()
+         */
+        static FHTKey51* New();
+
+        /**
+         *  @copybrief   LemmaObject::Delete()
+         *  @copydetails LemmaObject::Delete()
+         */
+        void Delete();
+
+        // ====================  OPERATORS     =======================
+
+        // ====================  OPERATIONS    =======================
+
+        Complex Zgauss(const int &ikk, const EMMODE &imode,
+                            const int &itype, const Real &rho,
+                            const Real &wavef, KernelEm1DBase *Kernel);
+
+        /// Computes related kernels, if applicable, otherwise this is
+        /// just a dummy function.
+        void ComputeRelated(const Real& rho, KernelEm1DBase* Kernel);
+
+        void ComputeRelated(const Real& rho, std::vector< KernelEm1DBase* > KernelVec);
+
+        void ComputeRelated(const Real& rho, KernelEM1DManager* KernelManager);
+
+        // ====================  ACCESS        =======================
+
+        // ====================  INQUIRY       =======================
+
+        protected:
+
+        // ====================  LIFECYCLE     =======================
+
+        /** Default protected constructor, use New */
+        FHTKey51 (const std::string& name);
+
+        /** Default protected destructor, use Delete */
+        ~FHTKey51 ();
+
+        /**
+         *  @copybrief   LemmaObject::Release()
+         *  @copydetails LemmaObject::Release()
+         */
+        void Release();
+
+        private:
+
+        // ====================  DATA MEMBERS  =========================
+
+        // Shared Filter Weights
+		static const Eigen::Matrix<Real, 51, 3>  WT51;
+
+        /// Holds answer, dimensions are NumConv, and NumberRelated.
+        Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic> Zans;
+
+    }; // -----  end of class  FHTKey51  -----
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef FHTKEY51_INC  -----
+

Modules/FDEM1D/include/GroundedElectricDipole.h

@@ -0,0 +1,87 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      01/29/2014 06:59:39 AM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+
+#ifndef  GROUNDEDELECTRICDIPOLE_INC
+#define  GROUNDEDELECTRICDIPOLE_INC
+
+#include "dipolesource.h"
+
+namespace Lemma {
+
+    /**
+      \brief   Grounded electric dipole
+      \details Used to model an idealised grounded electrid dipole of arbitrary
+               polarisation.
+     */
+    class GroundedElectricDipole : public DipoleSource {
+
+        friend std::ostream &operator<<(std::ostream &stream,
+                const GroundedElectricDipole &ob);
+
+        public:
+
+        // ====================  LIFECYCLE     =======================
+
+        /**
+         * @copybrief LemmaObject::New()
+         * @copydetails LemmaObject::New()
+         */
+        static GroundedElectricDipole* New();
+
+        /**
+         *  @copybrief   LemmaObject::Delete()
+         *  @copydetails LemmaObject::Delete()
+         */
+        void Delete();
+
+        // ====================  OPERATORS     =======================
+
+        // ====================  OPERATIONS    =======================
+
+        // ====================  ACCESS        =======================
+
+        // ====================  INQUIRY       =======================
+
+        protected:
+
+        // ====================  LIFECYCLE     =======================
+
+        /** Default protected constructor, use New */
+        GroundedElectricDipole (const std::string& name);
+
+        /** Default protected destructor, use Delete */
+        ~GroundedElectricDipole ();
+
+        /**
+         *  @copybrief   LemmaObject::Release()
+         *  @copydetails LemmaObject::Release()
+         */
+        void Release();
+
+        private:
+
+        // ====================  DATA MEMBERS  =========================
+
+    }; // -----  end of class  GroundedElectricDipole  -----
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef GROUNDEDELECTRICDIPOLE_INC  -----
+

Modules/FDEM1D/include/LayeredEarthEMReader.h

@@ -0,0 +1,105 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      09/27/2013 01:44:36 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2013, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2013, Trevor Irons
+ */
+
+#ifndef  LAYEREDEARTHEMREADER_INC
+#define  LAYEREDEARTHEMREADER_INC
+
+#include "LemmaObject.h"
+#include "ASCIIParser.h"
+#include "layeredearthem.h"
+
+namespace Lemma {
+
+    /**
+      \brief
+      \details
+     */
+    class LayeredEarthEMReader : public LemmaObject {
+
+        friend std::ostream &operator<<(std::ostream &stream,
+                const LayeredEarthEMReader &ob);
+
+        public:
+
+        // ====================  LIFECYCLE     =======================
+
+        /**
+         * @copybrief LemmaObject::New()
+         * @copydetails LemmaObject::New()
+         */
+        static LayeredEarthEMReader* New();
+
+        /**
+         *  @copybrief   LemmaObject::Delete()
+         *  @copydetails LemmaObject::Delete()
+         */
+        void Delete();
+
+        // ====================  OPERATORS     =======================
+
+        // ====================  OPERATIONS    =======================
+
+        /** Reads ASCII input file. The format is as follows
+@code
+4           // Number of NON-AIR layers
+200   10    // resistivity, thickness layer 1 [Ohm-m] [m]
+20    10    // resistivity, thickness layer 2 [Ohm-m] [m]
+1120  10    // resistivity, thickness layer 3 [Ohm-m] [m]
+200         // resistivity of bottom layer [Ohm-m]
+@endcode
+         * @param[in] name is the filename
+         */
+        void ReadASCIIInputFile( const std::string& name );
+
+        // ====================  ACCESS        =======================
+
+        /** @return the pointer address of the LayeredEarthEM
+         */
+        LayeredEarthEM* GetLayeredEarth();
+
+        // ====================  INQUIRY       =======================
+
+        protected:
+
+        // ====================  LIFECYCLE     =======================
+
+        /** Default protected constructor, use New */
+        LayeredEarthEMReader (const std::string& name);
+
+        /** Default protected destructor, use Delete */
+        ~LayeredEarthEMReader ();
+
+        /**
+         *  @copybrief   LemmaObject::Release()
+         *  @copydetails LemmaObject::Release()
+         */
+        void Release();
+
+        private:
+
+        // ====================  DATA MEMBERS  =========================
+
+        LayeredEarthEM*         LayEarth;
+
+    }; // -----  end of class  LayeredEarthEMReader  -----
+
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef LAYEREDEARTHEMREADER_INC  -----

Modules/FDEM1D/include/MagneticDipole.h

@@ -0,0 +1,88 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      09/25/2013 08:20:14 AM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2013, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2013, Trevor Irons
+ */
+
+#ifndef  MAGNETICDIPOLE_INC
+#define  MAGNETICDIPOLE_INC
+
+#include "dipolesource.h"
+
+namespace Lemma {
+
+/**
+  @class
+  \brief   Magnetic Dipole
+  \details Used to model an idealised magnetic dipole of arbitrary
+           polarisation.
+ */
+class MagneticDipole : public DipoleSource {
+
+    friend std::ostream &operator<<(std::ostream &stream,
+            const MagneticDipole &ob);
+
+    public:
+
+    // ====================  LIFECYCLE     =======================
+
+    /**
+     * @copybrief LemmaObject::New()
+     * @copydetails LemmaObject::New()
+     */
+    static MagneticDipole* New();
+
+    /**
+     *  @copybrief   LemmaObject::Delete()
+     *  @copydetails LemmaObject::Delete()
+     */
+    void Delete();
+
+    // ====================  OPERATORS     =======================
+
+    // ====================  OPERATIONS    =======================
+
+    // ====================  ACCESS        =======================
+
+    // ====================  INQUIRY       =======================
+
+    protected:
+
+    // ====================  LIFECYCLE     =======================
+
+    /** Default protected constructor, use New */
+    MagneticDipole (const std::string& name);
+
+    /** Default protected destructor, use Delete */
+    ~MagneticDipole ();
+
+    /**
+     *  @copybrief   LemmaObject::Release()
+     *  @copydetails LemmaObject::Release()
+     */
+    void Release();
+
+    private:
+
+    // ====================  DATA MEMBERS  =========================
+
+    KernelEM1DManager*          Kernels;
+
+}; // -----  end of class  MagneticDipole  -----
+
+} // namespace Lemma
+
+#endif   // ----- #ifndef MAGNETICDIPOLE_INC  -----

Modules/FDEM1D/include/PolygonalWireAntenna.h

@@ -0,0 +1,169 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     05/18/2010
+  @version  $Id: PolygonalWireAntenna.h 211 2015-02-27 05:43:26Z tirons $
+ **/
+
+#include "WireAntenna.h"
+
+#ifndef  POLYGONALWIREANTENNA_INC
+#define  POLYGONALWIREANTENNA_INC
+
+namespace Lemma {
+
+    // ===================================================================
+    //        Class:  PolygonalWireAntenna
+    /// \brief   Class representing polygonal wire antennae.
+    /// \details For EM calculations, dipoles representing this loop are
+    ///    created dynamically, depending on receiver location.
+    /// @todo enforce minimum dipole moment.
+    // ===================================================================
+    class PolygonalWireAntenna : public WireAntenna {
+
+        friend std::ostream &operator<<(std::ostream &stream,
+                const PolygonalWireAntenna &ob);
+
+        public:
+
+            // ====================  LIFECYCLE     =======================
+
+            /**
+             * Declares all memory and returns a new instance.
+             */
+            static PolygonalWireAntenna* New();
+
+            /**
+             * @copybrief LemmaObject::Delete()
+             * @copydetails LemmaObject::Delete()
+             */
+            void Delete();
+
+            /// Makes a deep copy of this antenna with all connections except
+            /// the dipole approximation.
+            PolygonalWireAntenna* Clone();
+
+            // ====================  OPERATORS     =======================
+
+            // ====================  OPERATIONS    =======================
+
+            /// Approximates with ungrounded electrical dipoles, such that
+            /// minDipoleRatio is satisfied.
+            virtual void ApproximateWithElectricDipoles(const Vector3r &rp);
+
+            /** Sets the minimum ratio for dipole moments to be used to
+             * approximate the loop. A smaller ratio yields a more accurate
+             * result, but is more expensive. Default is (1/5).
+             */
+            void SetMinDipoleRatio(const Real& ratio);
+
+            /** Sets the minimum moment for dipole moments to be used to
+             * approximate the loop.
+             */
+            void SetMinDipoleMoment(const Real& m);
+
+            /** Sets the minimum moment for dipole moments to be used to
+             * approximate the loop.
+             */
+            void SetMaxDipoleMoment(const Real& m);
+
+            // ====================  ACCESS        =======================
+
+            // ====================  INQUIRY       =======================
+
+            #ifdef HAVE_YAMLCPP
+            /**
+             *  Uses YAML to serialize this object.
+             *  @return a YAML::Node
+             */
+            YAML::Node Serialize() const;
+
+            /**
+             *   Constructs an object from a YAML::Node.
+             */
+            static PolygonalWireAntenna* DeSerialize(const YAML::Node& node);
+            #endif
+
+        protected:
+
+            // ====================  LIFECYCLE     =======================
+
+            /// Default protected constructor.
+            PolygonalWireAntenna (const std::string& name);
+
+#ifdef HAVE_YAMLCPP
+            /// Default protected constructor.
+            PolygonalWireAntenna (const YAML::Node& node);
+#endif
+
+            /// Default protected constructor.
+            ~PolygonalWireAntenna ();
+
+            /**
+             * @copybrief LemmaObject::Release()
+             * @copydetails LemmaObject::Release()
+             */
+            void Release();
+
+            // ====================  DATA MEMBERS  =======================
+
+            /// minimum ratio of dipole moment to distance to receiver point
+            Real minDipoleRatio;
+
+            /// Maximum dipole moment allowed
+            Real minDipoleMoment;
+
+            /// Maximum dipole moment allowed
+            Real maxDipoleMoment;
+
+            /// appends
+            void PushXYZDipoles(const Vector3r &step, const Vector3r &cp,
+                            const Vector3r &dir,
+                            std::vector<DipoleSource*> &Dipoles) ;
+
+            /// corrects for overstep
+            void CorrectOverstepXYZDipoles(const Vector3r &step,
+                            const Vector3r &cp,
+                            const Vector3r &dir,
+                            std::vector<DipoleSource*> &Dipoles );
+
+            // ====================  OPERATIONS    =======================
+
+
+            /// Returns the nearest point on a line segment to another point.
+            /// if the point is not on the line-segment, return the
+            /// nearest end-point
+            /// @param[in] p0, p1 define the line segement
+            /// @param[in] rp is a point in space. The function returns the
+            /// closest point on the line to this point.
+            /// @return The point (Lemma::Vector3r) on the line defined by p0,
+            /// and p1, closest to rp
+            Vector3r ClosestPointOnLine(const Vector3r &p0, const Vector3r &p1,
+                            const Vector3r &rp);
+
+            /// Interpolates dipoles along line segment defined by p0 and p1.
+            void InterpolateLineSegment(const Vector3r &p0, const Vector3r &p1,
+                            const Vector3r &rp);
+
+
+            /// List of the dipoles
+            //std::vector<DipoleSource*>           Dipoles;
+
+            /// Points that define this loop
+            //Vector3Xr                            Points;
+
+        private:
+
+            Vector3r                               rRepeat;
+
+    }; // -----  end of class  PolygonalWireAntenna  -----
+
+}       // -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef POLYGONALWIREANTENNA_INC  -----

Modules/FDEM1D/include/QWEKey.h

@@ -0,0 +1,197 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      02/12/2014 10:20:18 AM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#ifndef  QWEKEY_INC
+#define  QWEKEY_INC
+
+#include	"hankeltransform.h"
+#include    <Eigen/Eigenvalues>
+#ifdef HAVEBOOSTSPECIALFUNCTIONS
+#include "boost/math/special_functions.hpp"
+#include "boost/math/special_functions/bessel.hpp"
+#endif
+
+namespace Lemma {
+
+    /** breakpoint to use in division of domain, based on zeros of bessel function or
+        regular nPi spacing.
+     */
+    enum sZeroType{J0, J1, NPI};
+
+    /**
+      \brief  Port of Key's quadrature with extrapolation Hankel transform algorithm.
+      \details Details of the algorithm can be found in Key2011. This code is a port
+               of the published algorithm, which contains the following notice:
+        %------------------------------------------------------------------%
+        % Copyright (c) 2012 by the Society of Exploration Geophysicists.  %
+        % For more information, go to http://software.seg.org/2012/0003 .  %
+        % You must read and accept usage terms at:                         %
+        % http://software.seg.org/disclaimer.txt before use.               %
+        %------------------------------------------------------------------%
+     */
+    class QWEKey : public HankelTransform {
+
+        friend std::ostream &operator<<(std::ostream &stream,
+                const QWEKey &ob);
+
+        public:
+
+        // ====================  LIFECYCLE     =======================
+
+        /**
+         * @copybrief LemmaObject::New()
+         * @copydetails LemmaObject::New()
+         */
+        static QWEKey* New();
+
+        /**
+         *  @copybrief   LemmaObject::Delete()
+         *  @copydetails LemmaObject::Delete()
+         */
+        void Delete();
+
+        // ====================  OPERATORS     =======================
+
+        void TestPrivate(const int& N);
+
+        // ====================  OPERATIONS    =======================
+
+
+        Complex Zgauss(const int &ikk, const EMMODE &imode,
+                            const int &itype, const Real &rho,
+                            const Real &wavef, KernelEm1DBase *Kernel);
+
+        /// Computes related kernels, if applicable, otherwise this is
+        /// just a dummy function.
+        void ComputeRelated(const Real& rho, KernelEm1DBase* Kernel);
+
+        void ComputeRelated(const Real& rho, std::vector< KernelEm1DBase* > KernelVec);
+
+        void ComputeRelated(const Real& rho, KernelEM1DManager* KernelManager);
+
+        // ====================  ACCESS        =======================
+
+        // ====================  INQUIRY       =======================
+
+        protected:
+
+        // ====================  LIFECYCLE     =======================
+
+        /** Default protected constructor, use New */
+        QWEKey (const std::string& name);
+
+        /** Default protected destructor, use Delete */
+        ~QWEKey ();
+
+        /**
+         *  @copybrief   LemmaObject::Release()
+         *  @copydetails LemmaObject::Release()
+         */
+        void Release();
+
+        /** Calculates Gauss quadrature weights of order N on the interval -1,1
+            Algorithm from p 129 in:
+            Trefethen, L. N., 2000, Spectral methods in MATLAB: Society for
+            Industrial and Applied Mathematics (SIAM), volume 10 of Software,
+            Environments, and Tools.
+        */
+        void GaussQuadWeights(const int& N);
+
+        /** Returns the quadrature intervals and Bessel function weights used for the
+            QWE method.
+
+         */
+        void BesselWeights( const sZeroType& sType);
+
+        /**  Computes an infinite integral using the partial sum of quadrature terms
+             accelerated by sequence extrapolation using the Shanks transformation
+             implemented with Wynn's epsilon algorithm.
+         */
+        void QWE(const Real& rho);
+
+        /** Calls the underlying kernel functions evaluated as necessary
+         */
+        void getEyKernel(const int& i, const int& idx, const Real& rho);
+
+        private:
+
+        // ====================  DATA MEMBERS  =========================
+
+        /** Relative tolerance, default is 1e-6 */
+        Real    RelTol;
+
+        /** Absolute tolerance, default is 1e-24 */
+        Real    AbsTol;
+
+        /** Quadrature order, higher is more accurate but more expensive. Eefault is 9 */
+        int     nQuad;
+
+        /** in QWE partial integrals before Shanks recurive algorithm. Defaults to 1  */
+        int nDelay;
+
+        /** Maximum number of intervals to integrate over . Defaults to 40  */
+        int nIntervalsMax;
+
+        /** Weighing of gaussian quadrature points */
+        VectorXr GaussWeights;
+
+        /** Abscissa locations of quadrature points */
+        VectorXr GaussAbscissa;
+
+        /** Breakpoints for dividing up the global integral */
+        VectorXr xInt;
+
+        /** All quadrature points between all breakpoints */
+        VectorXr Bx;
+
+        /** J0 weights */
+        VectorXr BJ0;
+
+        /** J1 weights */
+        VectorXr BJ1;
+
+        /** array of lambda arguments */
+        VectorXr Lambda;
+
+        /** array of lambda arguments */
+        VectorXr Intervals;
+
+        MatrixXcr TS;
+        VectorXi  Tn;
+        MatrixXcr Textrap;
+        MatrixXr  TrelErr;
+        MatrixXr  TabsErr;
+
+        /** Container to hold bessel arguments */
+        Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic > Zwork;
+
+        /** Container to hold bessel arguments */
+        Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic > Zans;
+
+        /** Manager for related kernels to evaluate */
+        KernelEM1DManager* KernelManager;
+
+    }; // -----  end of class  QWEKey  -----
+
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef QWEKEY_INC  -----
+
+

Modules/FDEM1D/include/UngroundedElectricDipole.h

@@ -0,0 +1,88 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      01/29/2014 08:52:43 AM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+
+#ifndef  UNGROUNDEDELECTRICDIPOLE_INC
+#define  UNGROUNDEDELECTRICDIPOLE_INC
+
+#include "dipolesource.h"
+
+namespace Lemma {
+
+    /**
+      \brief  Ungrounded electric dipole
+      \details Used to model an idealised ungrounded electric dipole. Used primarily in integrating
+                around current sources.
+     */
+    class UngroundedElectricDipole : public DipoleSource {
+
+        friend std::ostream &operator<<(std::ostream &stream,
+                const UngroundedElectricDipole &ob);
+
+        public:
+
+        // ====================  LIFECYCLE     =======================
+
+        /**
+         * @copybrief LemmaObject::New()
+         * @copydetails LemmaObject::New()
+         */
+        static UngroundedElectricDipole* New();
+
+        /**
+         *  @copybrief   LemmaObject::Delete()
+         *  @copydetails LemmaObject::Delete()
+         */
+        void Delete();
+
+        // ====================  OPERATORS     =======================
+
+        // ====================  OPERATIONS    =======================
+
+        // ====================  ACCESS        =======================
+
+        // ====================  INQUIRY       =======================
+
+        protected:
+
+        // ====================  LIFECYCLE     =======================
+
+        /** Default protected constructor, use New */
+        UngroundedElectricDipole (const std::string& name);
+
+        /** Default protected destructor, use Delete */
+        ~UngroundedElectricDipole ();
+
+        /**
+         *  @copybrief   LemmaObject::Release()
+         *  @copydetails LemmaObject::Release()
+         */
+        void Release();
+
+        private:
+
+        // ====================  DATA MEMBERS  =========================
+
+    }; // -----  end of class  UngroundedElectricDipole  -----
+
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef UNGROUNDEDELECTRICDIPOLE_INC  -----
+

Modules/FDEM1D/include/WireAntenna.h

@@ -0,0 +1,249 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     12/16/2009
+  @version  $Id: WireAntenna.h 201 2015-01-03 00:07:47Z tirons $
+ **/
+
+#ifndef __WIREANTENNA_H
+#define __WIREANTENNA_H
+
+#include "LemmaObject.h"
+#include "dipolesource.h"
+
+#ifdef LEMMAUSEVTK
+#include "vtkActor.h"
+#endif
+
+namespace Lemma {
+
+
+    // ===================================================================
+    /**      Class:  WireAntenna
+      * \brief   Class representing a wire antennae.
+      * \details This is an abstract class.
+	  */
+    // ===================================================================
+    class WireAntenna : public LemmaObject {
+
+        friend std::ostream &operator<<(std::ostream &stream,
+            const WireAntenna &ob);
+
+        public:
+
+            // ====================  LIFECYCLE     =======================
+
+            /**
+             * Initialises antenna to contain no points, with no current
+             * and no frequency. NumberOfTurns set to 1
+             */
+            static WireAntenna* New();
+
+            /**
+             * Provides deep copy
+             */
+            virtual WireAntenna* Clone();
+
+            /**
+             * @copybrief LemmaObject::Delete()
+             * @copydetails LemmaObject::Delete()
+             */
+            void Delete();
+
+            // ====================  OPERATORS     =======================
+
+            // ====================  OPERATIONS    =======================
+
+            /**
+              * Approximates with evenly spaced electric dipoles around loop
+              * @param[in] delta is the spacing between moments
+			  */
+            virtual void ApproximateWithElectricDipoles(const Real &delta);
+
+            // ====================  ACCESS        =======================
+
+			/**
+              * Sets the number of turns in the loop, default is 1
+              * @param[in] nturns is the number of turns of the loop.
+			  */
+            void SetNumberOfTurns(const int &nturns);
+
+            /**
+              * Sets the number of points in the loop
+			  */
+            void SetNumberOfPoints(const int &np);
+
+			/**
+              * Sets a corner point of the loop. Counting starts at 0. It
+              * is not required to have the loop be closed right now, but
+              * its a good idea.
+			  */
+            void SetPoint(const int &p, const Vector3r &pos);
+
+            /**
+              * Sets a corner point of the loop. Counting starts at 0. It
+              * is not required to have the loop be closed right now, but
+              * its a good idea.
+			  */
+            void SetPoint(const int &p, const Real&x, const Real& y, const Real& z);
+
+            /** Sets the frequency of the current in the loop, default is 0
+			  * @param[in] ifreq is the frequency number to set
+              * @param[in] freq is the frequency (Hz) of the current
+			  */
+            void SetFrequency(const int& ifreq, const Real &freq);
+			/**
+              * Sets the number of frequencies.
+              * @param[in] nfreq is the number of frequencies that will be
+              * computed.
+			  */
+            void SetNumberOfFrequencies(const int& nfreq);
+
+			/**
+              * Sets the current in the loop, default is 0
+              * @param[in] amp is the current in the loop, in Amperes
+			  */
+            void SetCurrent(const Real &amp);
+
+            // ====================  INQUIRY       =======================
+
+            #ifdef HAVE_YAMLCPP
+            /**
+             *  Uses YAML to serialize this object.
+             *  @return a YAML::Node
+             */
+            YAML::Node Serialize() const;
+
+            /**
+             *   Constructs an object from a YAML::Node.
+             */
+            static WireAntenna* DeSerialize(const YAML::Node& node);
+            #endif
+
+			/**
+              * Returns the number of turns
+              * @return the number of turns of the loop.
+			  */
+            int GetNumberOfTurns( );
+
+            /**
+             * Returns all of the points
+             */
+            Vector3Xr GetPoints();
+
+            /**
+             * Returns all of the points in a general matrix, useful for python wrapper
+             */
+            MatrixXr GetPointsMat();
+
+			/**
+              * Returns the frequency in the loop.
+              * @return is the frequency in the loop in Hz
+			  */
+            Real GetFrequency(const int& ifreq);
+
+
+			/**
+              * Returns the current in the loop.
+              * @return is the Current
+			  */
+            Real GetCurrent( );
+
+
+			/**
+              * Returns pointer to a dipole source
+			  */
+            DipoleSource* GetDipoleSource(const int &dip);
+
+			/**
+              * returns number of dipoles used to approximate this
+              * loop
+			  */
+            int GetNumberOfDipoles();
+
+			/**
+              * @return the number of frequencies of this wire loop.
+			  */
+            int GetNumberOfFrequencies();
+
+            #ifdef LEMMAUSEVTK
+            /** Returns an actor that can be placed into a vtk scene easily
+              * Note that this function throws a pointer, it is the
+              * receivers job to manage this memory!
+			  */
+            vtkActor* GetVtkActor(const int &idip);
+            #endif
+
+            /** Returns true or false if loop is horizontally planar
+             */
+            bool IsHorizontallyPlanar();
+
+        protected:
+
+            // ====================  LIFECYCLE     =======================
+
+			/**
+              * Default protected constructor.
+			  */
+            WireAntenna (const std::string &name);
+
+#ifdef HAVE_YAMLCPP
+        /** Protected DeDerializing constructor, use factory DeSerialize  method*/
+            WireAntenna (const YAML::Node& node);
+#endif
+
+			/**
+              * Default protected destructor.
+			  */
+            ~WireAntenna ();
+
+            /**
+             * @copybrief LemmaObject::Release()
+             * @copydetails LemmaObject::Release()
+             */
+            void Release();
+
+            // ====================  DATA MEMBERS  =======================
+
+			/**
+              * Number of points that define the loop
+			  */
+            int NumberOfPoints;
+
+			/**
+              * Current in antennae (Amps)
+			  */
+            Real Current;
+
+			/**
+              * Number of turns
+			  */
+            int NumberOfTurns;
+
+			/**
+              * List of the dipoles
+			  */
+            std::vector<DipoleSource*>           Dipoles;
+
+			/**
+              * Points that define this loop
+			  */
+            Vector3Xr                            Points;
+
+			/**
+              * Frequencies of the loop.
+			  */
+            VectorXr                             Freqs;
+
+        private:
+
+    }; // -----  end of class  WireAntenna  -----
+
+}
+#endif // __WIREANTENNA_H

Modules/FDEM1D/include/emearth1d.h

@@ -0,0 +1,232 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     12/02/2009
+  @version  $Id: emearth1d.h 266 2015-04-01 03:24:00Z tirons $
+ **/
+
+#ifndef __EMEARTH1D_H
+#define __EMEARTH1D_H
+
+#include "dipolesource.h"
+#include "layeredearthem.h"
+#include "receiverpoints.h"
+#include "WireAntenna.h"
+#include "PolygonalWireAntenna.h"
+#include "kernelem1dspec.h"
+#include "kernelem1dmanager.h"
+#include "hankeltransformgaussianquadrature.h"
+#include "hankeltransformhankel2.h"
+#include "FHTKey.h"
+#include "FHTKey51.h"
+#include "FHTKey101.h"
+#include "QWEKey.h"
+#include "CubicSplineInterpolator.h"
+
+#ifdef HAVEBOOSTPROGRESS
+#include "boost/progress.hpp"
+#endif
+
+namespace Lemma {
+
+    // =======================================================================
+    //        Class:  EmEarth1D
+    /// \brief  Implimentation of 1D EM solution.
+    /// \details  We've done a lot of different things.
+    // =======================================================================
+    class EMEarth1D : public LemmaObject {
+
+		friend std::ostream &operator<<(std::ostream &stream,
+			const EMEarth1D &ob);
+
+        public:
+
+            //friend class KernelEm1D;
+
+            // ====================  LIFECYCLE     ===========================
+
+            /**
+             *  Returns pointer to new EMEarth1D. Location is
+             *  initialized to (0,0,0) type and polarization are
+             *  initialized  to nonworking values that will throw
+             *  exceptions if used.
+             */
+            static EMEarth1D* New();
+
+            /**
+             * @copybrief LemmaObject::Delete()
+             * @copydetails LemmaObject::Delete()
+             */
+            void Delete();
+
+            /** stream debugging info to std::out
+             */
+            void Query();
+
+            #ifdef HAVE_YAMLCPP
+            /** YAML Serializing method
+             */
+            YAML::Node Serialize() const;
+
+            //static EMEarth1D* DeSerialize(const YAML::Node& node);
+            #endif
+
+            // ====================  OPERATORS     ===========================
+
+            // ====================  OPERATIONS    ===========================
+
+            /// Calculates the field(s) due to an ungrounded dipole source
+            /// Calls FORTRAN library em1d (em1dnew.for)
+#ifdef COMPILE_FORTRAN
+            void MakeCalc();
+#endif
+
+            /** C++ wrapper for em1dnew.for, serial */
+            void MakeCalc3();
+
+            /** Calculates the field(s) due to a wire antennae */
+            void CalculateWireAntennaFields(bool progressbar=false);
+
+            // ====================  ACCESS        ===========================
+
+            /** Attaches an antennae */
+            void AttachWireAntenna(WireAntenna *antennae);
+
+            /** Attaches a dipole for calculation */
+            void AttachDipoleSource(DipoleSource *dipole);
+
+            /** Attaches a layered earth model for calculation */
+            void AttachLayeredEarthEM(LayeredEarthEM *Earth);
+
+            /** Attaches a set of receiver points for calculation */
+            void AttachReceiverPoints(ReceiverPoints *Receivers);
+
+            /** Sets the fields that are calcultated, E,H or BOTH */
+            void SetFieldsToCalculate(const FIELDCALCULATIONS &calc);
+
+            /** Sets the method to use to evaluate the Hankel integral,
+             */
+            void SetHankelTransformMethod(const HANKELTRANSFORMTYPE &type);
+
+            // ====================  INQUIRY       ===========================
+
+        protected:
+
+            // ====================  LIFECYCLE     ===========================
+
+            /** Default protected constructor. */
+            EMEarth1D (const std::string& name);
+
+            #ifdef HAVE_YAMLCPP
+            /** Default protected constructor. */
+			EMEarth1D (const YAML::Node& node);
+            #endif
+
+            /** Default protected constructor. */
+            ~EMEarth1D ();
+
+            /**
+             * @copybrief LemmaObject::Release()
+             * @copydetails LemmaObject::Release()
+             */
+            void Release();
+
+            // ====================  OPERATIONS    ===========================
+
+            /** Used internally, this is the innermost loop of the MakeCalc3,
+             *  and CalculateWireAntennaField routines.
+             */
+            void SolveSingleTxRxPair(const int &irec,
+                    HankelTransform *Hankel,
+                    const Real &wavef, const int &ifreq,
+                    DipoleSource *tDipole);
+
+            /** Used internally, this is the innermost loop of the MakeCalc3,
+             *  and CalculateWireAntennaField routines.
+             */
+            void SolveLaggedTxRxPair(const int &irec, Hankel2* Hankel,
+                    const Real &wavef, const int &ifreq,
+                    PolygonalWireAntenna* antenna);
+
+            /** Removes all connections */
+            void DetachAll();
+
+            // ====================  DATA MEMBERS  ===========================
+
+            /** Computes field due to dipole */
+            DipoleSource*        Dipole;
+
+            /** Earth model (Cole-cole) */
+            LayeredEarthEM*      Earth;
+
+            /** Receiver points */
+            ReceiverPoints*      Receivers;
+
+            /** Wire antennae tx */
+            WireAntenna*         Antenna;
+
+            /** What fields are wanted */
+            FIELDCALCULATIONS    FieldsToCalculate;
+
+            /** The type of Hankel transform to use, default to digital
+             *  filtering
+             */
+            HANKELTRANSFORMTYPE  HankelType;
+
+            /** Counter for number of caclulations made
+             */
+            int icalcinner;
+
+            /** Counter for number of caclulations made
+             */
+            int icalc;
+
+    }; // -----  end of class  EMEarth1D  -----
+
+    /////////////////////////////////////////
+    // Exception classes
+
+    /** If a Receivers Class is NULL valued, throw this.
+     */
+    class NullReceivers : public std::runtime_error {
+            /** Thrown when Receivers pointer is NULL
+             */
+            public: NullReceivers();
+    };
+
+    /** If an Antenna is NULL valued, throw this error.
+     */
+    class NullAntenna : public std::runtime_error {
+            /** Thrown when an antenna pointer is NULL
+             */
+            public: NullAntenna();
+    };
+
+    /** If an Instrument is NULL valued, throw this error.
+     */
+    class NullInstrument : public std::runtime_error {
+            /** thrown when an instrument pointer is NULL.
+             *  @param[in] ptr is a pointer to the class throwing the exception.
+             */
+            public: NullInstrument(LemmaObject* ptr);
+    };
+
+    /** If a dipole source is specified, but a method calling a wire antenna is
+     * called, throw this.
+     */
+    class DipoleSourceSpecifiedForWireAntennaCalc : public std::runtime_error {
+            /** Thrown when a dipole source is specified when a wire antenna is
+             * expected
+             */
+            public: DipoleSourceSpecifiedForWireAntennaCalc();
+    };
+
+} // Namespace Lemma
+
+#endif // __EMEARTH1D_H

Modules/FDEM1D/include/gaussianquadrature.h

@@ -0,0 +1,139 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     10/07/2010
+  @version  $Id: gaussianquadrature.h 193 2014-11-10 23:51:41Z tirons $
+ **/
+
+#ifndef __gaussianquadrature_h
+#define __gaussianquadrature_h
+
+#include "LemmaObject.h"
+
+namespace Lemma {
+
+
+	// ===================================================================
+	//        Class:  gaussianquadrature
+	/// \brief Numerical integration via Legendre-Gauss Quadrature.
+	/// \details Returns integration result, weights, and abscissae.  This
+	/// script computes the Legendre-Gauss nodes and weights on an interval
+	/// [a,b] with truncation order N.  This class is heavily derived from
+	/// lgwt.m by Greg von Winckel (2/25/2004).
+	// ===================================================================
+	class gaussianquadrature {
+
+		public:
+
+			friend std::ostream &operator<<(std::ostream &stream,
+						const gaussianquadrature &ob);
+
+			// ====================  LIFECYCLE     =======================
+
+			static gaussianquadrature* New();
+
+			void Delete();
+
+			// ====================  OPERATORS     =======================
+
+			// ====================  OPERATIONS    =======================
+			/// Perform Gaussian Quadrature Integration
+			void Integrate();
+
+			/// Calculate abscissae and weights
+			void CalcAW();
+
+			// ====================  ACCESS        =======================
+			/// Set number of points and limits
+			void SetFreqs(const int& nfreq, const Real& a, const Real& b);
+
+			/// Eigen Vector of function values to be integrated over
+			void SetFunc(const VectorXr& fx);
+
+			// ====================  INQUIRY       =======================
+			/// Returns Eigen Vector of Abscissae
+			VectorXr GetAbscissae();
+
+			/// Returns Eigen Vector of Weights
+			VectorXr GetWeights();
+
+			/// Returns integration result
+			Real GetResult();
+
+
+		protected:
+
+			// ====================  LIFECYCLE     =======================
+
+			/// Default protected constructor.
+			gaussianquadrature ();
+
+			/// Default protected constructor.
+			~gaussianquadrature ();
+
+
+
+			// ====================  DATA MEMBERS  =========================
+			/// Interval
+			Real dx;
+
+			/// Machine precision
+			Real machineeps;
+
+			/// Bookkeeping variable
+			int N;
+
+			/// Bookkeeping variable
+			int N1;
+
+			/// Bookkeeping variable
+			int N2;
+
+			/// Lower bound
+			Real a;
+
+			/// Upper bound
+			Real b;
+
+			/// Placeholder vector
+			VectorXr ytemp;
+
+			/// Abscissae
+			VectorXr xu;
+
+			/// Intermediate Abscissae vector
+			VectorXr y;
+
+			/// Intermediate Abscissae vector
+			VectorXr y0;
+
+			/// Legendre-Gauss Vandermonde Matrix
+			MatrixXr L;
+
+			/// Derivative of LGVM
+			VectorXr Lp;
+
+			/// Intermediate Matrix
+			VectorXr Ltemp;
+
+			/// Weights Vector
+			VectorXr wgq;
+
+			///Function to integrate
+			VectorXr funcx;
+
+			/// Integration result
+			Real intres;
+
+		private:
+
+	}; // -----  end of class  gaussianquadrature  -----
+} // end of namespace Lemma
+#endif // __gaussianquadrature_h
+

Modules/FDEM1D/include/hankeltransform.h

@@ -0,0 +1,90 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     01/28/2010
+  @version  $Id: hankeltransform.h 270 2015-08-24 15:45:41Z tirons $
+ **/
+
+#ifndef __hankeltransform_h
+#define __hankeltransform_h
+
+#include "LemmaObject.h"
+#include "kernelem1dbase.h"
+#include "kernelem1dspec.h"
+#include "kernelem1dmanager.h"
+
+namespace Lemma {
+
+        // ===================================================================
+        //        Class:  HankelTransform
+        /// \brief  Pure abstract class for hankel transforms
+        /// \details
+        // ===================================================================
+        class HankelTransform : public LemmaObject {
+
+            public:
+
+                /// Prints out basic info about the class
+                friend std::ostream &operator<<(std::ostream &stream,
+                        const HankelTransform &ob);
+
+                // ====================  LIFECYCLE     =======================
+
+                //static HankelTransform* New();
+
+                //void Delete();
+
+                // ====================  OPERATORS     =======================
+
+                // ====================  OPERATIONS    =======================
+
+                /// @todo this is actually a deprecated function. Only Chave
+                ///   uses this.
+                /// Performs numerical integration using Gaussian quadrature
+                /// ikk:   type of kernel depending on source and receiver couple
+                /// imode: a switch for TE(0) and TM(1) mode
+                /// itype: order of Bessel function
+                /// rho is argument to integral
+                /// wavef is the propogation constant of free space
+                /// = omega * sqrt( EP*AMU )  amu = 4 pi e-7  ep = 8.85e-12
+                virtual Complex Zgauss(const int &ikk, const EMMODE &imode,
+                            const int &itype, const Real &rho,
+                            const Real &wavef, KernelEm1DBase *Kernel)=0;
+
+                /// Computes related kernels, if applicable, otherwise this is
+                /// just a dummy function.
+                virtual void ComputeRelated(const Real& rho, KernelEm1DBase* Kernel);
+
+                virtual void ComputeRelated(const Real& rho, std::vector< KernelEm1DBase* > KernelVec);
+
+                virtual void ComputeRelated(const Real& rho, KernelEM1DManager* KernelManager);
+
+                // ====================  ACCESS        =======================
+
+                // ====================  INQUIRY       =======================
+
+                // ====================  DATA MEMBERS  =======================
+
+            protected:
+
+                // ====================  LIFECYCLE     =======================
+
+                /// Default protected constructor.
+                HankelTransform (const std::string &name);
+
+                /// Default protected constructor.
+                ~HankelTransform ();
+
+            private:
+
+    }; // -----  end of class  HankelTransform  -----
+
+}
+
+#endif // __hankeltransform_h

Modules/FDEM1D/include/hankeltransformgaussianquadrature.h

@@ -0,0 +1,349 @@
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     01/02/2010
+  @version  $Id: hankeltransformgaussianquadrature.h 199 2014-12-29 19:25:20Z tirons $
+ **/
+
+#ifndef  _HANKELTRANSFORMGAUSSIANQUADRATURE_h_INC
+#define  _HANKELTRANSFORMGAUSSIANQUADRATURE_h_INC
+
+#include "hankeltransform.h"
+#include "kernelem1dbase.h"
+
+#ifdef HAVEBOOSTCYLBESSEL
+#include "boost/math/special_functions.hpp"
+#endif
+
+namespace Lemma {
+
+
+	// =======================================================================
+	//        Class:  HankelTransformGaussianQuadrature
+	/// \brief  Calculates hankel transform using gaussian quadrature.
+	/// \details  Accurate but slow, this is a port of Alan Chave's public domain
+    /// fortran code
+	// =======================================================================
+	class HankelTransformGaussianQuadrature : public HankelTransform {
+
+		friend std::ostream &operator<<(std::ostream &stream,
+				const HankelTransformGaussianQuadrature &ob);
+
+		public:
+
+			// ====================  LIFECYCLE     ===========================
+
+            /**
+             *  Returns pointer to new HankelTransformGaussianQuadrature.
+             *  Location is
+             *  initialized to (0,0,0) type and polarization are
+             *  initialized  to nonworking values that will throw
+             *  exceptions if used.
+             */
+			static HankelTransformGaussianQuadrature* New();
+
+            /**
+             * @copybrief LemmaObject::Delete()
+             * @copydetails LemmaObject::Delete()
+             */
+            void Delete();
+
+			// ====================  OPERATORS     ===========================
+
+			// ====================  OPERATIONS    ===========================
+
+			/// Performs numerical integration using Gaussian quadrature
+			/// ikk:   type of kernel depending on source and receiver couple
+			/// imode: a switch for TE(0) and TM(1) mode
+			/// itype: order of Bessel function
+			/// rho is argument to integral
+			/// wavef is the propogation constant of free space
+			/// = omega * sqrt( EP*AMU )  amu = 4 pi e-7  ep = 8.85e-12
+            //template <EMMODE T>
+			Complex Zgauss(const int &ikk, const EMMODE &imode,
+							const int &itype, const Real &rho,
+							const Real &wavef, KernelEm1DBase *Kernel);
+
+			// ====================  ACCESS        ============================
+
+			// ====================  INQUIRY       ============================
+
+			// ====================  DATA MEMBERS  ============================
+
+		protected:
+
+			// ====================  LIFECYCLE     ============================
+
+			/// Default protected constructor.
+			HankelTransformGaussianQuadrature (const std::string &name);
+
+            /// Default protected constructor.
+			~HankelTransformGaussianQuadrature ();
+
+            /**
+             * @copybrief LemmaObject::Release()
+             * @copydetails LemmaObject::Release()
+             */
+            void Release();
+
+			// ====================  OPERATIONS    ============================
+
+			/// Modified by Yoonho Song to branch cut, June, 1996
+			/// Separate Gaussian quarature integral by two interval
+			/// first:  integal from 0 to wavenumber of free space
+			/// second: integral from wavenunmber of free space to infinity
+			///         for large arguments, it uses continued fraction also
+			/// It is recommended to use nl = 1 to 6, nu =7
+			/// PERFORMS AUTOMATIC CALCULATION OF BESSEL TRANSFORM TO SPECIFIED
+			/// RELATIVportisheadE AND ABSOLUTE ERROR
+			///
+			/// ARGUMENT LIST:
+			///
+			/// BESR,BESI-REAL AND IMAGINARY PARTS RETURNED BY BESAUX
+			/// iorder-ORDER OF THE BESSEL FUNCTION
+			/// NL-LOWER LIMIT FOR GAUSS ORDER TO START COMPUTATION
+			/// NU-UPPER LIMIT FOR GAUSS ORDER
+			/// NU,NL=1,...7 SELECTS 3,7,15,31,63,127,AND 255 POINT GAUSS
+			/// QUADRATURE BETWEEN THE ZERO CROSSINGS OF THE BESSEL FUNCTION
+			/// R-ARGUMENT OF THE BESSEL FUNCTION
+			/// RERR,AERR-RELATIVE AND ABSOLUTE ERROR FOR TERMINATION
+			/// BESAUX TERMINATES WHEN INCREASING THE GAUSS ORDER DOES NOT
+			/// CHANGE THE RESULT BY MORE THAN RERR OR WHEN THE ABSOLUTE ERROR
+			/// IS LESS THAN AERR OR WHEN A GAUSS ORDER OF NU IS REACHED.
+			/// NPCS-NUMBER OF PIECES INTO WHICH EACH PARTIAL INTEGRAND
+			/// IS DIVIDED,
+			/// ORDINARILY SET TO ONE. FOR VERY SMALL VALUES OF R WHERE
+			/// THE KERNEL FUNCTION IS APPRECIABLE ONLY OVER THE FIRST FEW
+			/// LOOPS OF THE BESSEL FUNCTION, NPCS MAY BE INCREASED TO ACHIEVE
+			/// REASONABLE ACCURACY.
+			/// NEW  IF NEW=1, THE INTEGRANDS ARE COMPUTED AND SAVED AT EACH
+			/// GAUSS
+			/// ORDER. IF NEW=2, PREVIOUSLY COMPUTED INTEGRANDS ARE USED. NOTE
+			/// THAT ORDER,R, AND NPCS MUST NOT BE CHANGED WHEN SETTING NEW=2.
+			/// IERR-ERROR PARAMETER
+			/// IERR=0--NORMAL RETURN
+			/// IERR=1--RESULT NOT ACCURATE TO RERR DUE TO TOO LOW A GAUSS
+			///  ORDER OR CONVERGENCE NOT ACHIEVED IN BESTRX
+            //template <EMMODE T>
+			void Besautn(Real &besr, Real &besi, const int &iorder,
+							const int &nl, const int &nu, const Real &rho,
+							const Real &rerr, const Real &aerr,
+							const int &npcs, int &inew, const Real &aorb,
+							KernelEm1DBase *Kernel);
+
+			/// COMPUTES BESSEL TRANSFORM OF SPECIFIED ORDER DEFINED AS
+			/// INTEGRAL(FUNCT(X)*J-SUB-ORDER(X*R)*DX) FROM X=0 TO INFINITY
+			/// COMPUTATION IS ACHIEVED BY INTEGRATION BETWEEN THE ASYMPTOTIC
+			/// ZERO CROSSINGS OF THE BESSEL FUNCTION USING GAUSS QUADRATURE.
+			/// THE RESULTING SERIES OF PARTIAL INTEGRANDS IS SUMMED BY
+			/// CALCULATING THE PADE APPROXIMANTS TO SPEED UP CONVERGENCE.
+			/// ARGUMENT LIST:
+			/// BESR,BESI  REAL AND IMAGINARY PARTS RETURNED BY BESTRN
+			/// iorder  ORDER OF THE BESSEL FUNCTIONC  NG  NUMBER OF GAUSS
+			/// POINTS TO USE IN THE QUADRATURE ROUTINE.
+			/// NG=1 THROUGH 7 SELECTS 3,7,15,31,63,126,AND 255 TERMS.
+			///   R     ARGUMENT OF THE BESSEL FUNCTION
+			///   RERR,AERR  SPECIFIED RELATIVE AND ABSOLUTE ERROR FOR THE
+			///           CALCULATION.  THE INTEGRATION
+			///  TERMINATES WHEN AN ADDITIONAL TERM DOES NOT CHANGE THE
+			///  RESULT BY MORE THAN RERR*RESULT+AERR
+			///  NPCS  NUMBER OF PIECES INTO WHICH EACH PARTIAL I
+			///        NTEGRAND IS DIVIDED,
+			///        ORDINARILY SET TO ONE. FOR VERY SMALL VALUES OF RANGE
+			///        WHERE THE KERNEL FUNCTION IS APPRECIABLE ONLY OVER THE
+			///        FIRST FEW LOOPS OF THE BESSEL FUNCTION, NPCS MAY BE
+			///        INCREASED TO ACHIEVE REASONABLE ACCURACY. NOTE THAT
+			///        NPCS AFFECTS ONLY THE PADE
+			///        SUM PORTION OF THE INTEGRATION, OVER X(NSUM) TO INFINITY.
+			/// XSUM  VECTOR OF VALUES OF THE KERNEL ARGUMENT OF FUNCT FOR WHICH
+			/// EXPLICIT CALCULATION OF THE INTEGRAL IS DESIRED, SO THAT THE
+			/// INTEGRAL OVER 0 TO XSUM(NSUM) IS ADDED TO THE INTEGRAL OVER
+			/// XSUM(NSUM) TO INFINITY WITH THE PADE METHOD INVOKED ONLY FOR
+			/// THE LATTER. THIS ALLOWS THE PADE SUMMATION METHOD TO BE
+			/// OVERRIDDEN AND SOME TYPES OF SINGULARITIES TO BE HANDLED.
+			/// NSUM  NUMBER OF VALUES IN XSUM, MAY BE ZERO.
+			/// NEW   DETERMINES METHOD OF KERNEL CALCULATION
+			/// NEW=0 MEANS  CALCULATE BUT DO NOT SAVE INTEGRANDS
+			/// NEW=1 MEANS CALCULATE KERNEL BY CALLING FUNCT-SAVE KERNEL
+			///       TIMES BESSEL FUNCTION
+			/// NEW=2 MEANS USE SAVED KERNELS TIMES BESSEL FUNCTIONS IN
+			///       COMMON /BESINT/. NOTE THAT ORDER,R,NPCS,XSUM, AND
+			///       NSUM MAY NOT BE CHANGED WHEN SETTING NEW=2.
+			/// IERR  ERROR PARAMETER
+			///       0 NORMAL RETURN-INTEGRAL CONVERGED
+			///       1 MEANS NO CONVERGENCE AFTER NSTOP TERMS IN THE PADE SUM
+			///
+			/// SUBROUTINES REQUIRED:
+			/// BESQUD,PADECF,CF,ZEROJ,DOT,JBESS
+			///  A.CHAVE IGPP/UCSD
+			/// NTERM IS MAXIMUM NUMBER OF BESSEL FUNCTION LOOPS STORED IF
+			/// NEW.NE.0
+			/// NSTOP IS MAXIMUM Number of Pade terms
+            //template <EMMODE T>
+ 			void Bestrn( Real &BESR, Real &BESI, const int &iorder,
+ 					const int &NG, const Real &R,
+ 					const Real &RERR, const Real &AERR, const int &npcs,
+ 					VectorXi &XSUM, int &NSUM, int &NEW,
+ 					int &IERR, int &NCNTRL, const Real &AORB,
+					KernelEm1DBase *Kernel);
+
+			/// CALCULATES THE INTEGRAL OF F(X)*J-SUB-N(X*R) OVER THE
+			/// INTERVAL A TO B AT A SPECIFIED GAUSS ORDER THE RESULT IS
+			/// OBTAINED USING A SEQUENCE OF 1, 3, 7, 15, 31, 63, 127, AND 255
+			/// POINT INTERLACING GAUSS FORMULAE SO THAT NO INTEGRAND
+			/// EVALUATIONS ARE WASTED. THE KERNEL FUNCTIONS MAY BE
+			/// SAVED SO THAT BESSEL TRANSFORMS OF SIMILAR KERNELS ARE COMPUTED
+			/// WITHOUT NEW EVALUATION OF THE KERNEL.  DETAILS ON THE FORMULAE
+			/// ARE GIVEN IN 'THE OPTIMUM ADDITION OF POINTS TO QUADRATURE
+			/// FORMULAE' BY T.N.L. PATTERSON, MATHS.COMP. 22,847-856 (1968).
+			/// GAUSS WEIGHTS TAKEN FROM COMM. A.C.M. 16,694-699 (1973)
+			/// ARGUMENT LIST:
+			/// A      LOWER LIMIT OF INTEGRATION
+			/// B      UPPER LIMIT OF INTEGRATION
+			/// BESR,BESI RETURNED INTEGRAL VALUE REAL AND IMAGINARY PARTS
+			/// NG NUMBER OF POINTS IN THE GAUSS FORMULA.  NG=1,...7
+			///        SELECTS 3,7,15,31,63,127,AND 255 POINT QUADRATURE.
+			///  NEW SELECTS METHOD OF KERNEL EVALUATION
+			///    NEW=0 CALCULATES KERNELS BY CALLING F - NOTHING SAVED
+			///    NEW=1 CALCULATES KERNELS BY CALLING F AND SAVES KERNEL TIMES
+			///           BESSEL FUNCTION IN COMMON /BESINT/
+			///    NEW=2 USES SAVED KERNEL TIMES BESSEL FUNCTIONS IN
+			///           COMMON /BESINT/
+			/// iorder ORDER OF THE BESSEL FUNCTION
+			/// R    ARGUMENT OF THE BESSEL FUNCTION
+			/// F     F(X) IS THE EXTERNAL INTEGRAND SUBROUTINE
+			/// A.CHAVE IGPP/UCSDC
+			/// MAXIMUM NUMBER OF BESSEL FUNCTION LOOPS THAT CAN BE SAVED
+            //template <EMMODE T>
+			void Besqud(const Real &A, const Real &B, Real &BESR, Real &BESI,
+							const int &NG, const int &NEW, const int &iorder,
+							const Real &R, KernelEm1DBase *Kernel);
+
+			/// COMPUTES SUM(S(I)),I=1,...N BY COMPUTATION OF PADE APPROXIMANT
+			/// USING CONTINUED FRACTION EXPANSION.  FUNCTION IS DESIGNED TO BE
+			/// CALLED SEQUENTIALLY AS N IS INCREMENTED FROM 1 TO ITS FINAL
+			/// VALUE.  THE NTH CONTINUED FRACTION COEFFICIENT IS CALCULATED AND
+			/// STORED AND THE NTH CONVERGENT RETURNED.  IT IS UP TO THE USER TO
+			/// STOP THE CALCULATION WHEN THE DESIRED ACCURACY IS ACHIEVED.
+			/// ALGORITHM FROM HANGGI ET AL., Z.NATURFORSCH. 33A,402-417 (1977)
+			/// IN THEIR NOTATION, VECTORS CFCOR,CFCOI ARE LOWER CASE D,
+			/// VECTORS DR, DI ARE UPPER CASE D, VECTORS XR,XI ARE X, AND
+			/// VECTORS SR,SI ARE S
+			/// A.CHAVE IGPP/UCSD
+			void Padecf(Real &SUMR, Real &SUMI, const int &N);
+
+			/// EVALUATES A COMPLEX CONTINUED FRACTION BY RECURSIVE DIVISION
+			/// STARTING AT THE BOTTOM, AS USED BY PADECF
+			/// RESR,RESI ARE REAL AND IMAGINARY PARTS RETURNED
+			/// CFCOR,CFCOI ARE REAL AND IMAGINARY VECTORS OF CONTINUED FRACTION
+			/// COEFFICIENTS
+			void CF(        Real& RESR, Real &RESI,
+							Eigen::Matrix<Real, 100, 1> &CFCOR,
+							Eigen::Matrix<Real, 100, 1> &CFCOI,
+							const int &N);
+
+
+			/// COMPUTES ZERO OF BESSEL FUNCTION OF THE FIRST KIND FROM
+			/// MCMAHON'S ASYMPTOTIC EXPANSION
+			/// NZERO-NUMBER OF THE ZERO
+			/// iorder-ORDER OF THE BESSEL FUNCTION (0 OR 1)
+			Real ZeroJ(const int &ZERO, const int &IORDER);
+
+			/// COMPUTES BESSEL FUNCTION OF ORDER "ORDER" AND ARGUMENT X BY
+			/// CALLING NBS ROUTINES J0X AND J1X (REAL*8 BUT APPROXIMATELY
+			/// REAL*4 ACCURACY).
+			/// FOR MORE ACCURACY JBESS COULD BE CHANGED TO CALL, FOR EXAMPLE,
+			/// THE IMSL ROUTINES MMBSJ0,MMBSJ1 << SEE C// BELOW >>
+			Real Jbess(const Real &X, const int &IORDER);
+
+			/// COMPUTES DOT PRODUCT OF TWO D.P. VECTORS WITH NONUNIT
+			/// INCREMENTING ALLOWED. REPLACEMENT FOR BLAS SUBROUTINE SDOT.
+			/// Currently does no checking, kind of stupid.
+			/// The fortran version will wrap around if (inc*N) > X1.size()
+			/// but not in a nice way.
+			Real _dot(const int&N,
+				const Eigen::Matrix<Real, Eigen::Dynamic, Eigen::Dynamic> &X1,
+							const int &INC1,
+				const Eigen::Matrix<Real, Eigen::Dynamic, Eigen::Dynamic> &X2,
+				const int &INC2);
+
+			// ====================  DATA MEMBERS  ============================
+
+            static const Real PI2;
+			static const Real X01P;
+			static const Real XMAX;
+			static const Real XSMALL;
+			static const Real J0_X01;
+			static const Real J0_X02;
+			static const Real J0_X11;
+			static const Real J0_X12;
+			static const Real FUDGE;
+			static const Real FUDGEX;
+			static const Real TWOPI1;
+			static const Real TWOPI2;
+			static const Real RTPI2;
+			static const Real XMIN;
+			static const Real J1_X01;
+			static const Real J1_X02;
+			static const Real J1_X11;
+			static const Real J1_X12;
+
+			/// Highest gauss order used, Was NG
+			int HighestGaussOrder;
+
+			/// Total number of partial integrals on last call, was NI
+			int NumberPartialIntegrals;
+
+			/// Total number of function calls, was NF
+			int NumberFunctionEvals;
+
+			int          np;
+			int          nps;
+
+            /////////////////////////////////////////////////////////////
+			// Eigen members
+
+            // Shared constant values
+			static const VectorXr  WT;
+			static const VectorXr  WA;
+
+			Eigen::Matrix<int,  100, 1>    Nk;
+			//Eigen::Matrix<Real, 255, 100>  karg;
+			//Eigen::Matrix<Real, 510, 100>  kern;
+			Eigen::Matrix<Real, Eigen::Dynamic, Eigen::Dynamic>  karg;
+			Eigen::Matrix<Real, Eigen::Dynamic, Eigen::Dynamic>  kern;
+
+			// Was Besval COMMON block
+			Eigen::Matrix<Real, 100, 1> Xr;
+			Eigen::Matrix<Real, 100, 1> Xi;
+			Eigen::Matrix<Real, 100, 1> Dr;
+			Eigen::Matrix<Real, 100, 1> Di;
+			Eigen::Matrix<Real, 100, 1> Sr;
+			Eigen::Matrix<Real, 100, 1> Si;
+			Eigen::Matrix<Real, 100, 1> Cfcor;
+			Eigen::Matrix<Real, 100, 1> Cfcoi;
+
+		private:
+
+	}; // -----  end of class  HankelTransformGaussianQuadrature  -----
+
+    //////////////////////////////////////////////////////////////
+    // Exception Classes
+
+    /** If the lower integration limit is greater than the upper limit, throw this
+     * error.
+     */
+    class LowerGaussLimitGreaterThanUpperGaussLimit :
+        public std::runtime_error {
+        /** Thrown when the LowerGaussLimit is greater than the upper limit.
+         */
+        public: LowerGaussLimitGreaterThanUpperGaussLimit();
+    };
+
+}	   // -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef _HANKELTRANSFORMGAUSSIANQUADRATURE_h_INC  -----

Modules/FDEM1D/include/hankeltransformhankel2.h

@@ -0,0 +1,246 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     06/26/2009
+  @version  $Id: hankeltransformhankel2.h 201 2015-01-03 00:07:47Z tirons $
+ **/
+
+#ifndef __HANKEL2_H
+#define __HANKEL2_H
+
+#include "hankeltransform.h"
+#include "kernelem1dbase.h"
+#include "kernelem1dspec.h"
+#include "CubicSplineInterpolator.h"
+
+namespace Lemma {
+
+// ==========================================================================
+//        Class:  Hankel2
+/** \brief   Computes the Hankel transform of orders 0 and 1 using lagged
+             and related convolutions.
+    \details A rewrite of work by Anderson who wrote a FORTRAN program
+             that he released while working at the USGS.
+             The  transform evaluates an integral of the form:
+             \f[ \int_0^\infty K(\lambda) J_I (\lambda r) ~ d \lambda
+             \f]
+             Where \f$ K(\lambda) \f$ is some kernel function. The value
+             \f$ J_I \f$ is the Bessel function of order
+             \f$I, I \in \{0,1\} \f$
+             The kernel function is unique for each source and is computed
+             in the class CalculateKernel. The value \f$r\f$ is the radial
+             distance away from the centre of the grid \f$ r=\sqrt{x^2 + y^2} \f$
+             The Hankel transform is useful as it allows a double fourier
+             transform to be written as a single integral:
+             \f[ \mathop {\int \!\!\! \int}_{\!\!\!\!\!-\infty}^{\,\,\infty}
+             F(k_x^2 + k_y^2)
+                 e^{\imath (k_x x + k_y y)} dk_x \, dk_y = 2 \pi
+                 \int_0^\infty K(\lambda) J_I (\lambda r) ~ d \lambda
+             \f]
+             This can only be done where there is radial symmetry. Hence
+             its application to 1D solutions here.
+ */
+// ==========================================================================
+
+class Hankel2 : public HankelTransform {
+
+    friend std::ostream &operator<<(std::ostream &stream, const Hankel2 &ob);
+
+    public:
+
+        // ====================  LIFECYCLE     ==============================
+        /**
+         *  Returns pointer to new Hankel2. Location is
+         *  initialized to (0,0,0) type and polarization are
+         *  initialized  to nonworking values that will throw
+         *  exceptions if used.
+         */
+        static Hankel2 *New();
+
+        /**
+         * @copybrief LemmaObject::Delete()
+         * @copydetails LemmaObject::Delete()
+         */
+        void Delete();
+
+        // ====================  OPERATORS     ==============================
+
+        // ====================  OPERATIONS    ==============================
+
+        /// Sets the number of convolutions
+        void SetNumConv(const int &i);
+
+        /// Computes the hankel transform with arguments
+        /// @param rho [input] rho is the hankel transform argument
+        /// @param ntol [input] ntol is
+        /// @param tol [input] tol is
+        void Compute(const Real &rho, const int& ntol, const Real &tol);
+
+        /// Computes the related
+        void ComputeRelated(const Real &rho, KernelEm1DBase* Kernel);
+
+        /// Computes the related
+        void ComputeRelated(const Real &rho,  std::vector< KernelEm1DBase* > KernelVec);
+
+        /// Computes the related
+        void ComputeRelated(const Real &rho,  KernelEM1DManager* Manager);
+
+        /// Computes the related and lagged convolutions
+        void ComputeLaggedRelated(const Real &rho, const int& nlag,  KernelEM1DManager* Manager);
+
+        // ====================  ACCESS        ==============================
+
+        /// Returns the answer
+        Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic>  GetAnswer();
+
+        /// Returns the arguments for lagged convolutions
+        VectorXr GetArg() {return Arg;};
+
+        /// Returns the value of Abscissa stepping
+        Real GetABSER( ) { return ABSER; };
+
+        /// Sets the lagged kernel index so that the proper value is returned
+        void SetLaggedArg(const Real& rho);
+
+
+        // ====================  INQUIRY       ==============================
+
+        /// Calculates Hankel Transform using filtering.
+        /// ikk:   type of kernel depending on source and receiver couple
+        /// imode: a switch for TE(0) and TM(1) mode
+        /// itype: order of Bessel function
+        /// rho is argument to integral
+        /// wavef is the propogation constant of free space
+        /// = omega * sqrt( EP*AMU )  amu = 4 pi e-7  ep = 8.85e-12
+        Complex Zgauss(const int &ikk, const EMMODE &imode,
+                        const int &itype, const Real &rho,
+                        const Real &wavef, KernelEm1DBase *Kernel);
+
+    protected:
+
+        // ====================  LIFECYCLE     ==============================
+
+        /** A rewrite of Anderson's Pseudo-subroutine. */
+        inline void StoreRetreive(const int &idx, const int &lag,
+                        Complex &Zsum, const int &irel, Complex &C, const Real& rho0) {
+
+            int look = idx+lag;
+    		int	iq = look/801;
+    		int	ir = look%801;
+    		int iroll = iq*800;
+
+    		if(this->Key[ir] <= iroll) {
+			    this->Key[ir] = iroll + ir;
+ 	    		++this->NumFun;
+                Manager->ComputeReflectionCoeffs(this->Lambda, idx, rho0);
+ 			    for (unsigned int ir2=0; ir2<this->kernelVec.size(); ++ir2) {
+ 			        this->Zwork(ir, ir2) = this->kernelVec[ir2]->RelBesselArg(this->Lambda);
+ 			    }
+		    }
+
+		    C = this->Zwork(ir, irel) * this->FilterWeights(this->BesselOrder, idx);
+		    Zsum += C;
+		    return;
+	    }
+
+        /// Default protected constructor
+        Hankel2(const std::string& name);
+
+        /// Default protected destructor
+        ~Hankel2();
+
+        /**
+         * @copybrief LemmaObject::Release()
+         * @copydetails LemmaObject::Release()
+         */
+        void Release();
+
+        // ====================  OPERATIONS    ==============================
+
+        void DeleteSplines();
+
+        // ====================  DATA MEMBERS  ==============================
+
+        /// The hankel transform wavenumber embedded in the integral
+        Real Lambda;
+
+        /// Number of times a kernel was evaluated
+        int NumFun;
+
+        /// Number of lagged convolutions
+        /// must be greater or equal to 1
+        /// It is set automatically in the @see Compute function so
+        /// that  \f$ \rho \exp\left( -.1*(\mathtt{NumConv} -1) \right) \f$
+        /// does not underflow the exponent range
+        int NumConv;
+
+        /// Number of related kernels
+        int NumRel;
+
+        /** Bessel transform order to use */
+        int BesselOrder;
+
+        /** Lag argument */
+        int iLag;
+
+        /* Should results be cached? Useful for repeated calculations of few receiver points */
+        // turned out to have only marginal benefits in best case, and awful consequences in many
+        //bool cacheResults;
+
+        /** Related Kernel Manager */
+        KernelEM1DManager*          Manager;
+
+        /// Used as base for filter abscissa generation
+        static const Real ABSCISSA;
+
+        /// Also used in abscissa generation \f$ ABSE = \exp{.1} \f$
+        static const Real ABSE;
+
+        /// Also used in abscissa generation \f$ ABSER = 1 / \exp{.1} \f$
+        static const Real ABSER;
+
+        /// Counter for calculated
+        int icount;
+
+        /// Kernel Calculator
+        std::vector <KernelEm1DBase*> kernelVec;
+
+        /// Spines for lagged convolutions (real part)
+        std::vector <CubicSplineInterpolator*> splineVecReal;
+
+        /// Spines for lagged convolutions (imaginary part)
+        std::vector <CubicSplineInterpolator*> splineVecImag;
+
+        /// Key used internally
+        Eigen::Matrix<int, 801, 1> Key;
+        //int  Key[801];
+        //Eigen::Matrix<int, Eigen::Dynamic, 1> Key;
+
+        /// Filter weight coefficients. Set for either \f$J_0\f$ or \f$J_1\f$
+        /// internally by protected function SetFilterWeights.
+        /// Fixed sized will yield better performance. (not necessarily)
+        //Eigen::Matrix<Real, 801, 1> FilterWeights;
+        static const Eigen::Matrix<Real, 2, 801> FilterWeights;
+        //static const Eigen::Matrix<Real, Eigen::Dynamic, Eigen::Dynamic> FilterWeights;
+
+        /// Zwork from Anderson
+        Eigen::Matrix<Complex, 801, Eigen::Dynamic> Zwork;
+        //Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic> Zwork;
+
+        /// Holds answer, dimensions are NumConv, and NumberRelated.
+        Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic> Zans;
+
+        /// Holds the arguments for lagged convolutions
+        VectorXr Arg;
+
+}; // -----  end of class  HankelTransform  -----
+
+}
+
+#endif // __HANKEL2_h

Modules/FDEM1D/include/instrumentfem.h

@@ -0,0 +1,144 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   M. Andy Kass
+  @date     01/14/2013
+  @version  $Id$
+ **/
+
+#ifndef __INSTRUMENTFEM_H
+#define __INSTRUMENTFEM_H
+
+#include "instrument.h"
+#include "emearth1d.h"
+#include "WireAntenna.h"
+#include "PolygonalWireAntenna.h"
+#include "receiverpoints.h"
+#include "dipolesource.h"
+#include "layeredearthem.h"
+#include "datafem.h"
+
+namespace Lemma {
+
+// ===================================================================
+//        Class:  InstrumentFem
+/// \brief
+/// \details
+// ===================================================================
+	class InstrumentFem : public Instrument {
+		friend std::ostream &operator<<(std::ostream &stream,
+			const InstrumentFem &ob);
+
+
+	public:
+
+	// ====================  LIFECYCLE     =======================
+
+		static InstrumentFem* New();
+
+		void Delete();
+
+	// ====================  OPERATORS     =======================
+
+	// ====================  OPERATIONS    =======================
+
+		/// Make the forward model calculation
+		void MakeCalculation();
+
+		/// Forward model from a vector of inputs
+		void ForwardModelProfile();
+
+	// ====================  ACCESS        =======================
+	//
+		/// Set layered earth model
+		void EMEarthModel(LayeredEarthEM* Earth);
+
+		/// Set dipole source
+		void SetDipoleSource(DipoleSource* dipolesource);
+
+		/// Set Field Points
+		void SetReceiverPoints(ReceiverPoints* receiver);
+
+		/// Copy parameters from data object
+		void AlignWithData(DataFEM* inpdata);
+
+		/// Set a data object for output
+		void SetOutputData(DataFEM* outputdata);
+
+
+
+	// ====================  INQUIRY       =======================
+
+
+	protected:
+
+	// ====================  LIFECYCLE     =======================
+
+		/// Default protected constructor.
+		InstrumentFem (const std::string &name);
+
+		/// Default protected constructor.
+		~InstrumentFem ();
+
+		void Release();
+
+	// ====================  DATA MEMBERS  =========================
+
+	LayeredEarthEM* EarthModel;
+
+	DipoleSource* Dipole;
+
+	ReceiverPoints* Receiver;
+
+	DataFEM* InputData;
+
+	DataFEM* OutputData;
+
+	/// Vector of dipole sources - may be superceded by boost
+	std::vector<DipoleSource*> Transmitters;
+
+	/// Vector of receivers - may be superceded by boost
+	/// not necessary--one set of receivers for all dipoles,
+	/// except the number of frequencies is built into the receiver
+	std::vector<ReceiverPoints*> Receivers;
+
+	/// Vector of Earth Models - may be superceded by boost
+	//std::vector<LayeredEarthEM*> EarthModels;
+
+	/// Number of frequencies
+	int nFreq;
+
+	/// Number of observation locations
+	int nObs;
+
+	/// Array of frequencies
+	VectorXr freq;
+
+	/// Position vector, with z as height above the ground surface (pos)
+	Vector3Xr xyz;
+
+	/// Array of Tx orientations (x,y,z) for each freq
+	Eigen::Matrix<ORIENTATION,Eigen::Dynamic,1> TxOrientation;
+
+	/// Array of Rx orientations (x,y,z) for each freq
+	Eigen::Matrix<ORIENTATION,Eigen::Dynamic,1> RxOrientation;
+
+	/// Transmitter moments, one for each frequency
+	VectorXr TxMom;
+
+	/// Tx/Rx Separation in local, right hand system with x aligned with flight
+	Vector3Xr TxRxSep;
+
+	/// Scale factor as described in EM1DFM manual
+	VectorXr ScaleFac;
+
+	private:
+
+}; // -----  end of class  InstrumentFem  -----
+} // end of namespace Lemma
+#endif

Modules/FDEM1D/include/integrationkernel.h

@@ -0,0 +1,92 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     02/07/2011
+  @version  $Id: integrationkernel.h 193 2014-11-10 23:51:41Z tirons $
+ **/
+
+#ifndef  INTEGRATIONKERNEL_INC
+#define  INTEGRATIONKERNEL_INC
+
+#include "LemmaObject.h"
+
+namespace Lemma {
+
+    // ===================================================================
+    //  Class:  IntegrationKernel
+    /**
+      @class
+      \brief    Abstract class that computes arguments for numerical
+                integrators.
+      \details  Needs to provide Argument function, as well as be able to
+                set necessary integration parameters.
+     */
+    // ===================================================================
+    template <typename T>
+    class IntegrationKernel : public LemmaObject {
+
+        public:
+
+            // ====================  LIFECYCLE     =======================
+
+
+            // ====================  OPERATORS     =======================
+
+            // ====================  OPERATIONS    =======================
+
+            /** Returns the argument of a function at a given argument. Also
+             *  capable or returning related function values.
+             */
+            //template <typename T>
+            virtual T Argument(const Real& x, const int& iRelated)=0;
+
+            // ====================  ACCESS        =======================
+
+            // ====================  INQUIRY       =======================
+
+            virtual int GetNumRel()=0;
+
+        protected:
+
+            // ====================  LIFECYCLE     =======================
+
+            /// Default protected constructor.
+            IntegrationKernel (const std::string& name);
+
+            /// Default protected constructor.
+            ~IntegrationKernel ();
+
+            // ====================  DATA MEMBERS  =========================
+
+        private:
+
+    }; // -----  end of class  IntegrationKernel  -----
+
+    template <typename T>
+    IntegrationKernel<T>::IntegrationKernel(const std::string& name) :
+        LemmaObject(name) {
+    }
+
+    template<typename T>
+    IntegrationKernel<T>::~IntegrationKernel( ) {
+    }
+
+//     template <typename T>
+//     T IntegrationKernel<T>::Argument(const Real& x, const int& iRelated) {
+//         return 11.;
+//     }
+//
+//     template <typename T>
+//     int IntegrationKernel<T>::GetNumRel( ) {
+//         return 0;
+//     }
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef INTEGRATIONKERNEL_INC  -----

Modules/FDEM1D/include/inversesolver.h

@@ -0,0 +1,118 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     07/14/2010
+  @version  $Id: inversesolver.h 193 2014-11-10 23:51:41Z tirons $
+ **/
+
+#ifndef  INVERSESOLVER_H_INC
+#define  INVERSESOLVER_H_INC
+
+#include "LemmaObject.h"
+#include "data.h"
+#include "instrument.h"
+#include "octreegrid.h"
+
+namespace Lemma {
+
+
+    // ===================================================================
+    //  Class:  InverseSolver
+    /**
+      @class  InverseSolver
+      \brief   Abstract class for inverse problem solver.
+      \details General solution of inverse problems.
+     */
+    // ===================================================================
+    class InverseSolver : public LemmaObject {
+
+        friend  std::ostream &operator<<(std::ostream &stream,
+                const InverseSolver &ob);
+
+        friend class OctreeGrid;
+
+        public:
+
+            // ====================  LIFECYCLE     =======================
+
+            // ====================  OPERATORS     =======================
+
+            // ====================  OPERATIONS    =======================
+
+            // ====================  ACCESS        =======================
+
+            /** @brief Sets the obsered data, any instance of Data.
+             *  @details This may either be field data, or forward modelled
+             *  data.
+             *  @param[in] ObsData a pointer to the observed data class.
+             */
+            void SetObservedData(Data* ObsData);
+
+            /** @brief Sets the instument that is used to create the data.
+             *  @details This is used for all forward modelling.
+             *  @param[in] inst is a pointer to the instrument class.
+             */
+            void SetInstrument(Instrument* inst);
+
+            /** @brief Returns the predicted data.
+             *  @return a pointer to the predicted data.
+             */
+            Data* GetPredictedData();
+
+            // ====================  INQUIRY       =======================
+
+            /** Returns the number of iterations it took to converge to a
+             *  solution.
+             */
+            virtual int NumberOfIterations()=0;
+
+            /** Returns true if the inversion converged successfully.
+             */
+            virtual bool Success()=0;
+
+            /** Returns a vector of \f$ \phi_M \f$
+             */
+            virtual VectorXr GetPhiMVector()=0;
+
+            /** Returns a vector of \f$ \phi_D \f$
+             */
+            virtual VectorXr GetPhiDVector()=0;
+
+        protected:
+
+            // ====================  OPERATIONS    =======================
+
+            /// Used as a callback function from iterating mesh.
+            virtual void FillInG(const Vector3r& pos, const Vector3r& step)=0;
+
+            // ====================  LIFECYCLE     =======================
+
+            /// Default protected constructor.
+            InverseSolver (const std::string &name);
+
+            /// Default protected constructor.
+            ~InverseSolver ();
+
+            // ====================  DATA MEMBERS  =========================
+
+            /// The Observed Data
+            Data* ObservedData;
+
+            /// The Predicted Data
+            Data* PredictedData;
+
+            /// Instrument that makes the data
+            Instrument*            ModelInstrument;
+
+        private:
+
+    }; // -----  end of class  InverseSolver  -----
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef INVERSESOLVER_H_INC  -----

Modules/FDEM1D/include/kernel.h

@@ -0,0 +1,85 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     01/29/2010
+  @version  $Id: kernel.h 193 2014-11-10 23:51:41Z tirons $
+ **/
+
+#ifndef __kernel_h
+#define __kernel_h
+
+#ifdef LEMMAUSEVTK
+#include "vtkImplicitFunction.h"
+#endif
+
+#include "LemmaObject.h"
+#include "receivercubes.h"
+
+namespace Lemma {
+
+        // ==================================================================
+        //        Class:  Kernel
+        /// \brief Pure abstract class for some kind of kernel function.
+        /// \details Provides a consistent interface to kernel functions.
+        // ==================================================================
+        class Kernel : public LemmaObject {
+
+            /// Prints out basic info about the class
+            friend std::ostream &operator<<(std::ostream &stream,
+                        const Kernel &ob);
+
+            public:
+
+                // ====================  LIFECYCLE     ======================
+
+                //static Kernel* New();
+
+                virtual void Delete()=0;
+
+                // ====================  OPERATORS     ======================
+
+                // ====================  OPERATIONS    ======================
+
+                // ====================  ACCESS        ======================
+
+                // ====================  INQUIRY       ======================
+
+                virtual VectorXcr ComputeSensitivity()=0;
+
+                #ifdef LEMMAUSEVTK
+                virtual VectorXcr ComputeSensitivity(vtkImplicitFunction* Impl)=0;
+                #endif
+
+                /** computes sensitivity for same value */
+                virtual VectorXcr ComputeSensitivity(const Real& fval)=0;
+
+                /** Computes sensitivity for array of values */
+                virtual VectorXcr ComputeSensitivity(const VectorXr& fval)=0;
+
+                virtual void SetFieldCubes(ReceiverCubes* pts)=0;
+
+                // ====================  DATA MEMBERS  ======================
+
+            protected:
+
+                // ====================  LIFECYCLE     ======================
+
+                /// Default protected constructor.
+                Kernel (const std::string& name);
+
+                /// Default protected constructor.
+                ~Kernel ();
+
+        private:
+
+    }; // -----  end of class  Kernel  -----
+
+}
+
+#endif // __kernel_h

Modules/FDEM1D/include/kernelem1dbase.h

@@ -0,0 +1,111 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+
+  @author   Trevor Irons
+  @date     05/18/2012
+  @version  $Id: kernelem1dbase.h 193 2014-11-10 23:51:41Z tirons $
+ **/
+
+#ifndef  KERNELEM1DBASE_INC
+#define  KERNELEM1DBASE_INC
+
+#include "LemmaObject.h"
+
+namespace Lemma {
+
+    // Transverse electric or magnetic mode
+    enum EMMODE {TM, TE, NONE};
+
+    // ===================================================================
+    //  Class:  KernelEm1DBase
+    /**
+      @class
+      \brief   Pure virtual base class of KernelEm1D
+      \details Defines interface for HankelTransform classes
+     */
+    // ===================================================================
+    class KernelEm1DBase : public LemmaObject {
+
+        friend class KernelEM1DManager;
+
+        public:
+
+            // ====================  LIFECYCLE     =======================
+
+            // ====================  OPERATORS     =======================
+
+            // ====================  OPERATIONS    =======================
+
+            /** Returns the Complex bessel argument to be evaluated for a given
+			 * lambda value
+             */
+            virtual Complex BesselArg(const Real& lambda)=0;
+
+            /** Returns the complex bessel argument. Same as above, but does not
+             *  call reflection coefficient calculation in KernelEM1DReflBase.
+             *  @param[in] lambda is the hankel wave value.
+             */
+            virtual Complex RelBesselArg(const Real& lambda)=0;
+
+            // ====================  ACCESS        =======================
+            virtual void SetIk(const int& ik)=0;
+
+            virtual void SetMode(const EMMODE& mode)=0;
+
+            int GetManagerIndex() {
+                return this->managerIdx;
+            }
+
+            // ====================  INQUIRY       =======================
+            virtual int GetNumRel()=0;
+
+            virtual int GetBesselOrder()=0;
+
+            virtual Complex GetZm()=0;
+
+            virtual Complex GetYm()=0;
+
+            virtual Complex GetZs()=0;
+
+            virtual Complex GetKs()=0;
+
+        protected:
+
+            // ====================  LIFECYCLE     =======================
+
+            /// Default protected constructor.
+            KernelEm1DBase (const std::string& name) : LemmaObject(name)
+            {
+            }
+
+            /// Default protected constructor.
+            ~KernelEm1DBase () {
+                if (this->NumberOfReferences > 0)
+                    throw DeleteObjectWithReferences( this );
+            }
+
+            void Release() {
+                delete this;
+            }
+
+            // ====================  OPERATIONS    =======================
+
+
+            // ====================  DATA MEMBERS  =========================
+
+            /** Where does this kernel live on the vector managed by the manager */
+            int  managerIdx;
+
+        private:
+
+    }; // -----  end of class  KernelEm1DBase  -----
+
+} // namespace Lemma
+
+#endif   // ----- #ifndef KERNELEM1DBASE_INC  -----

Modules/FDEM1D/include/kernelem1dmanager.h

@@ -0,0 +1,217 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     06/26/2012
+  @version   0.0
+ **/
+
+#ifndef  KERNELEM1DMANAGER_INC
+#define  KERNELEM1DMANAGER_INC
+
+//#include "dipolesource.h"
+//#include "kernelem1dreflbase.h"
+#include "kernelem1dbase.h"
+#include "kernelem1dspec.h"
+
+namespace Lemma {
+
+    class DipoleSource;
+    class KernelEM1DReflBase;
+
+    // ===================================================================
+    //  Class:  KernelEM1DManager
+    /**
+      @class
+      \brief
+      \details
+     */
+    // ===================================================================
+    class KernelEM1DManager : public LemmaObject {
+
+        public:
+
+            friend std::ostream &operator<<(std::ostream &stream,
+                        const KernelEM1DManager &ob);
+
+            // ====================  LIFECYCLE     =======================
+
+            /** Returns a pointer to a new object of type KernelEM1DManager.
+             * It allocates all necessary memory.
+             */
+            static KernelEM1DManager* New();
+
+            /** Deletes this object. Delete also disconnects any
+             * attachments to this object.
+             */
+            void Delete();
+
+            // ====================  OPERATORS     =======================
+
+            // ====================  OPERATIONS    =======================
+
+            template<EMMODE Mode, int Ikernel, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
+            int AddKernel( );
+            /*
+            {
+
+                KernelEm1DSpec<Mode, Ikernel, Isource, Irecv>* NewKern =
+                    KernelEm1DSpec<Mode, Ikernel, Isource, Irecv>::New();
+                KernelVec.push_back( NewKern );
+                NewKern->managerIdx = KernelVec.size()-1;
+                switch (Mode) {
+                    case TE:
+                        if (TEReflBase == NULL) {
+                            TEReflBase = KernelEM1DReflSpec<TE, Isource, Irecv>::New();
+                            TEReflBase->Initialise(Earth);
+                            TEReflBase->SetUpSource(Dipole, ifreq);
+                            TEReflBase->SetUpReceiver( rx_z );
+                        }
+                        NewKern->SetReflBase(TEReflBase);
+                        break;
+                    case TM:
+                        if (TMReflBase == NULL) {
+                            TMReflBase = KernelEM1DReflSpec<TM, Isource, Irecv>::New();
+                            TMReflBase->Initialise(Earth);
+                            TMReflBase->SetUpSource(Dipole, ifreq);
+                            TMReflBase->SetUpReceiver( rx_z );
+                        }
+                        NewKern->SetReflBase(TMReflBase);
+                        break;
+                }
+                return static_cast<int>(KernelVec.size()-1);
+            }
+            */
+
+            void ResetSource(const int& ifreq);
+
+            /** For use in related Kernel calculations. This function calles
+             * ComputeReflectionCoeffs on TEReflBase and TMReflBase, if they
+             * exist. After this has been called, KernelEM1DBase::RelBesselArg() may be safely
+             * called. This method stores solutions of the same idx. rho0 is the intial lambda argument
+             */
+            void ComputeReflectionCoeffs(const Real& lambda, const int& idx, const Real& rho0);
+
+            /** Clears the vector of kernels */
+            void ClearVec() {
+                for (unsigned int ik=0; ik<this->KernelVec.size(); ++ik) {
+                    this->KernelVec[ik]->Delete();
+                }
+                KernelVec.clear();
+            }
+
+            // ====================  ACCESS        =======================
+
+            /** Sets the LayeredEarthEM class that will be used by the kernels.
+             */
+            void SetEarth( LayeredEarthEM*   Earth);
+
+            /** Sets the source of the kernels */
+            void SetDipoleSource( DipoleSource*   Dipole, const int& ifreq, const Real& rx_zin);
+
+            /** Returns pointer to specified kernel indice. Indices are assigned in the same
+                order as they are created by AddKernel.
+             */
+            KernelEm1DBase*    GetKernel(const unsigned int& ik);
+
+            /** Returns pointer to connected dipole.
+             */
+            DipoleSource*    GetDipole( );
+
+            inline std::vector<KernelEm1DBase*>  GetSTLVector() {
+                return KernelVec;
+            }
+
+            // ====================  INQUIRY       =======================
+
+        protected:
+
+            // ====================  LIFECYCLE     =======================
+
+            /** Default protected constructor. */
+            KernelEM1DManager (const std::string& name);
+
+            /** Default protected constructor. */
+            ~KernelEM1DManager ();
+
+            /**
+             * @copybrief LemmaObject::Release()
+             * @copydetails LemmaObject::Release()
+             */
+            void Release();
+
+            // ====================  DATA MEMBERS  =========================
+
+            /** List of KernelEm1D instances */
+            std::vector<KernelEm1DBase*>           KernelVec;
+
+            /** Reflection base used for TE mode */
+            KernelEM1DReflBase*                    TEReflBase;
+
+            /** Reflection base used for TM mode */
+            KernelEM1DReflBase*                    TMReflBase;
+
+            /** EmEarth Class */
+            LayeredEarthEM*                        Earth;
+
+            /** EM dipole souce */
+            DipoleSource*                          Dipole;
+
+            /** Frequency index for the sources */
+            int                                    ifreq;
+
+            /** Receiver height */
+            Real                                   rx_z;
+
+        private:
+
+    }; // -----  end of class  KernelEM1DManager  -----
+
+    // template methods
+    template<EMMODE Mode, int Ikernel, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
+    int KernelEM1DManager::AddKernel( ) {
+
+        KernelEm1DSpec<Mode, Ikernel, Isource, Irecv>* NewKern =
+                    KernelEm1DSpec<Mode, Ikernel, Isource, Irecv>::New();
+        KernelVec.push_back( NewKern );
+        NewKern->managerIdx = KernelVec.size()-1;
+        switch (Mode) {
+            case TE:
+                if (TEReflBase == NULL) {
+                    TEReflBase = KernelEM1DReflSpec<TE, Isource, Irecv>::New();
+                    TEReflBase->Initialise(Earth);
+                    TEReflBase->SetUpSource(Dipole, ifreq);
+                    TEReflBase->SetUpReceiver( rx_z );
+                }
+                NewKern->SetReflBase(TEReflBase);
+                break;
+            case TM:
+                if (TMReflBase == NULL) {
+                    TMReflBase = KernelEM1DReflSpec<TM, Isource, Irecv>::New();
+                    TMReflBase->Initialise(Earth);
+                    TMReflBase->SetUpSource(Dipole, ifreq);
+                    TMReflBase->SetUpReceiver( rx_z );
+                }
+                NewKern->SetReflBase(TMReflBase);
+                break;
+        }
+        return static_cast<int>(KernelVec.size()-1);
+     }
+
+
+//     /** Clears the vector of kernels */
+//     void ClearVec() {
+//         for (unsigned int ik=0; ik<this->KernelVec.size(); ++ik) {
+//             this->KernelVec[ik]->Delete();
+//         }
+//         KernelVec.clear();
+//     }
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef KERNELEM1DMANAGER_INC  -----

Modules/FDEM1D/include/kernelem1dreflbase.h

@@ -0,0 +1,253 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     05/18/2012
+  @version  $Id: kernelem1dreflbase.h 193 2014-11-10 23:51:41Z tirons $
+ **/
+
+#ifndef  KERNELEM1DREFLBASE_INC
+#define  KERNELEM1DREFLBASE_INC
+
+#include "dipolesource.h"
+#include "kernelem1dbase.h"
+#include "layeredearthem.h"
+//#include "kernelem1dspec.h"
+
+namespace Lemma {
+
+    //class DipoleSource;
+
+    enum DIPOLE_LOCATION { INAIR, INGROUND };
+
+    // forward declaration for friend
+    template<EMMODE Mode, int Ikernel, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
+    class KernelEm1DSpec;
+
+
+    // ===================================================================
+    //  Class:  KernelEM1DReflBase
+    /**
+      @class
+      \brief   Abstract class defining EM1DRefl class.
+      \details Derived classes are template specialized for optimal performance.
+     */
+    // ===================================================================
+    class KernelEM1DReflBase : public LemmaObject {
+
+        template<EMMODE Mode, int Ikernel, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
+        friend class KernelEm1DSpec;
+        friend class KernelEM1DManager;
+
+        public:
+
+            // ====================  LIFECYCLE     =======================
+
+            // ====================  OPERATORS     =======================
+
+            // ====================  OPERATIONS    =======================
+
+            void Initialise(LayeredEarthEM* EarthIn) {
+
+                nlay = EarthIn->GetNumberOfLayers();
+                zh = VectorXcr::Zero(nlay);
+                yh = VectorXcr::Zero(nlay);
+                u = VectorXcr::Zero(nlay);
+                cf = VectorXcr::Zero(nlay);    // nlay -1 (lay 0 empty)
+                rtu = VectorXcr::Zero(nlay);   // nlay -1 Interfaces only
+                rtd = VectorXcr::Zero(nlay);   // nlay -1 Interfaces only
+                kk = VectorXcr::Zero(nlay);
+                Zyu = VectorXcr::Zero(nlay);
+                Zyd = VectorXcr::Zero(nlay);
+                Zyi = VectorXcr::Zero(nlay);
+                th = VectorXcr::Zero(nlay);
+
+                // Don't attach Earth, because this is performance critical.
+                // Everying is internal, it's OK relax Frankie
+                //if (Earth != NULL) {
+                //    Earth->DetachFrom(this);
+                //    Earth = NULL;
+                //}
+                //EarthIn->AttachTo(this);
+                Earth = EarthIn;
+
+                LayerThickness.resize(nlay);
+                for (int ilay=0; ilay<nlay; ++ilay) {
+                    LayerThickness(ilay) =  Earth->GetLayerThickness(ilay);
+                }
+
+                LayerDepth.resize(nlay);
+                for (int ilay=0; ilay<nlay; ++ilay) {
+                    LayerDepth(ilay) =  Earth->GetLayerDepth(ilay);
+                }
+
+            }
+
+            void SetUpSource(DipoleSource *Dipole, const int &ifreq) {
+
+                zh(0) = Complex(0, Dipole->GetAngularFrequency(ifreq)*MU0);
+                yh(0) = Complex(0, Dipole->GetAngularFrequency(ifreq)*EPSILON0);
+                kk(0) = -zh(0) * yh(0);
+
+                Earth->EvaluateColeColeModel(Dipole->GetAngularFrequency(ifreq));
+
+                for (int ilay=1; ilay<Earth->GetNumberOfLayers(); ++ilay) {
+                    zh(ilay) = zh(0) * Earth->GetLayerSusceptibility(ilay);
+                    yh(ilay) = Earth->GetLayerConductivity(ilay) +
+                            yh(0)*Earth->GetLayerPermitivity(ilay);
+                    kk(ilay)   = -zh(ilay)*yh(ilay);
+                }
+
+                tx_z = Dipole->GetLocation(2);
+                lays = 0;
+                Real Depth(0);
+                for (int ilay=1; ilay<nlay; ++ilay) {
+                    if (tx_z > Depth) {
+                        lays = ilay;
+                    }
+                    Depth += LayerThickness(ilay);
+                }
+            }
+
+            void SetUpReceiver(const Real &rz) {
+                rx_z = rz;
+                Real Depth(0.);
+                layr = 0;
+                for (int ilay=1; ilay<Earth->GetNumberOfLayers(); ++ilay) {
+                    if (rx_z > Depth) {
+                        layr = ilay;
+                    }
+                    Depth += LayerThickness(ilay);
+                }
+            }
+
+            // ====================  ACCESS        =======================
+            Complex GetYm() {
+                return yh(layr);
+            }
+
+            Complex GetZm() {
+                return zh(layr);
+            }
+
+            Complex GetZs() {
+                return zh(lays);
+            }
+
+            Complex GetKs() {
+                return kk(lays);
+            }
+
+            // ====================  INQUIRY       =======================
+
+        protected:
+
+            // ====================  LIFECYCLE     =======================
+
+            /// Default protected constructor.
+            KernelEM1DReflBase (const std::string& name) : LemmaObject(name)
+            {
+            }
+
+            /// Default protected constructor.
+            ~KernelEM1DReflBase () {
+                if (this->NumberOfReferences > 0)
+                    throw DeleteObjectWithReferences( this );
+            }
+
+            void Release() {
+                delete this;
+            }
+
+            // ====================  OPERATIONS    =======================
+
+            /** Computes reflection coefficients. Depending on the
+             * specialisation, this will either be TM or TE mode.
+             */
+            virtual void ComputeReflectionCoeffs(const Real& lambda)=0;
+
+            /** Precomputes expensive calculations that are reused by insances
+             * of KernelEM1DSpec in the calculation of Related potentials.
+             */
+            virtual void PreComputePotentialTerms()=0;
+
+            // ====================  DATA MEMBERS  =========================
+
+			/// Bessel order, only 0 or 1 supported
+			int id; // Needs to be dim nRel, or separate
+
+            /// Layer the source is in
+			int lays;
+
+			/// Layer the receiver is in
+			int layr;
+
+			/// Number of Layers
+			int nlay;
+
+            /// Number of Related kernels to be computed
+            int nRelated;
+
+            /// Used in related kernel precompute calls
+            int relIud;
+
+			/// Receiver z position
+			Real rx_z;
+
+			/// Transmitter z position
+			Real tx_z;
+
+            /// bessel arg squared
+            Real rams;
+
+            /** Related part of con term */
+            Complex  relCon;
+
+            Complex  relenukadz;
+
+            Complex  relexp_pbs1;
+
+            Complex  relexp_pbs2;
+
+            Complex  rel_a;
+
+			/// TM or TE mode
+			EMMODE mode;
+
+            /// Pointer to layered earth
+            LayeredEarthEM *Earth;
+
+			Complex       uk;
+			Complex       um;
+			VectorXcr     cf;  // nlay
+			VectorXcr      u;  // nlay
+			VectorXcr     yh;  // nlay
+			VectorXcr     zh;  // nlay
+			VectorXcr     kk;  // nlay
+			VectorXcr    Zyu;  //(nlay); //Zyu.setZero();
+			VectorXcr    Zyd;  //(nlay); //Zyd.setZero();
+			VectorXcr    Zyi;  //(nlay); //Zyi.setZero();
+			VectorXcr     th;  //(nlay);
+			VectorXr     LayerThickness;
+			VectorXr     LayerDepth;
+
+			/// Reflection/Transmission coeffients for upgoing waves in a
+			/// layered earth model
+			VectorXcr    rtu;
+
+			/// Reflection/Transmission coeffients for downgoing waves in
+			/// a layered earth model
+			VectorXcr    rtd;
+
+        private:
+
+    }; // -----  end of class  KernelEM1DReflBase  -----
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef KERNELEM1DREFLBASE_INC  -----

Modules/FDEM1D/include/kernelem1dreflspec.h

@@ -0,0 +1,373 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     05/18/2012
+  @version  $Id: kernelem1dreflspec.h 123 2014-02-05 23:47:20Z tirons $
+ **/
+
+#ifndef  KERNELEM1DREFLSPEC_INC
+#define  KERNELEM1DREFLSPEC_INC
+
+#include "dipolesource.h"
+#include "kernelem1dreflbase.h"
+#include "layeredearthem.h"
+
+// #include<unordered_map> // for caching results
+
+namespace Lemma {
+
+    // forward declare
+    //struct cache;
+    // Simple container to hold reflection results
+    struct  cache {
+        Real                       rho0;
+        Real                       lambda[805];
+        Real                       rams[805];
+        Complex                    uk[805];
+        Complex                    um[805];
+        Real                       zh0i[805];
+        VectorXcr                  Rtd[805];
+        VectorXcr                  Rtu[805];
+        VectorXcr                  u[805];
+        VectorXcr                  cf[805];
+        VectorXcr                  kk[805];
+        const Real                 epsilon;
+        //bool                       nc;
+        cache( ) : epsilon (std::numeric_limits<Real>::epsilon() ) { // TODO reset to precision of Real
+            //Rtd = VectorXcr::Zero(805);
+            //Rtu = VectorXcr::Zero(805);
+        }
+    };
+
+    // forward declaration for friend
+    template<EMMODE Mode, int Ikernel, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
+    class KernelEm1DSpec;
+
+    // ===================================================================
+    //  Class:  KernelEM1DReflSpec
+    /**
+      @class
+      \brief   Specialized version of KernelEM1DReflBase
+      \details Through use of template specialisations, this KernelEm1D
+               class delivers much better performance.
+     */
+    // ===================================================================
+    template<EMMODE Mode, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
+    class KernelEM1DReflSpec : public KernelEM1DReflBase {
+
+        public:
+
+            template<EMMODE Mode2, int Ikernel2, DIPOLE_LOCATION Isource2, DIPOLE_LOCATION Irecv2>
+            friend class KernelEm1DSpec;
+            friend class KernelEM1DManager;
+
+            // ====================  LIFECYCLE     =======================
+
+            static KernelEM1DReflSpec* New() {
+                KernelEM1DReflSpec<Mode, Isource, Irecv>*  Obj =
+                    new KernelEM1DReflSpec<Mode, Isource, Irecv>("KernelEM1DReflSpec<>");
+                Obj->AttachTo(Obj);
+                return Obj;
+            }
+
+            void Delete() {
+                this->DetachFrom(this);
+            }
+
+            // ====================  OPERATORS     =======================
+
+            // ====================  OPERATIONS    =======================
+
+            // ====================  ACCESS        =======================
+
+            // ====================  INQUIRY       =======================
+
+        protected:
+
+            // ====================  LIFECYCLE     =======================
+
+            /// Default protected constructor.
+            KernelEM1DReflSpec (const std::string& name) : KernelEM1DReflBase(name)
+            {
+            }
+
+            /// Default protected constructor.
+            ~KernelEM1DReflSpec () {
+                if (this->NumberOfReferences > 0)
+                    throw DeleteObjectWithReferences( this );
+            }
+
+            void Release() {
+                delete this;
+            }
+
+            // ====================  OPERATIONS    =======================
+
+            /** Computes reflection coefficients. Depending on the
+             * specialisation, this will either be TM or TE mode.
+             */
+            void ComputeReflectionCoeffs(const Real &lambda);
+
+            /* Computes reflection coefficients. Depending on the
+             * specialisation, this will either be TM or TE mode. This method
+             * stores previous results in a struct. For a given index, and
+             * lambda, the result will be the same. Turned out to be of limited utility.
+             */
+            //void ComputeReflectionCoeffs(const Real &lambda, const int& idx);
+
+            /** Precomputes expensive calculations that are reused by insances
+             * of KernelEM1DSpec in the calculation of Related potentials. This
+             * method is specialised based on template parameters
+             */
+            void PreComputePotentialTerms();
+
+            /*
+             * Sets the cache in CACHE to use. Somewhat expensive, avoid calling in tight loops
+             */
+            //void SetTCache(const Real& rho0);
+
+            // ====================  DATA MEMBERS  =========================
+
+        private:
+
+            //** Storage container for reused results */
+            //static std::unordered_map<Real, cache> CACHE;
+
+            //** Currenly used cache */
+            //cache* tcache;
+            //#pragma omp threadprivate(tcache)
+
+    }; // -----  end of class  KernelEM1DReflSpec  -----
+
+    //template<EMMODE Mode, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
+    //std::unordered_map<Real, cache> KernelEM1DReflSpec<Mode, Isource, Irecv>::CACHE;
+
+    //template<EMMODE Mode, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
+    //cache*  KernelEM1DReflSpec<Mode, Isource, Irecv>::tcache;
+
+    ///////////////////////////////////////////////
+    // Declarations of specialisations
+
+    template<>
+    void KernelEM1DReflSpec<TM, INAIR, INAIR>::ComputeReflectionCoeffs(const Real& lambda);
+
+    template<>
+    void KernelEM1DReflSpec<TE, INAIR, INAIR>::ComputeReflectionCoeffs(const Real& lambda);
+
+    template<>
+    void KernelEM1DReflSpec<TM, INAIR, INGROUND>::ComputeReflectionCoeffs(const Real& lambda);
+
+    template<>
+    void KernelEM1DReflSpec<TE, INAIR, INGROUND>::ComputeReflectionCoeffs(const Real& lambda);
+
+    template<>
+    void KernelEM1DReflSpec<TM, INAIR, INAIR>::PreComputePotentialTerms( );
+
+    template<>
+    void KernelEM1DReflSpec<TE, INAIR, INAIR>::PreComputePotentialTerms( );
+
+    template<>
+    void KernelEM1DReflSpec<TM, INAIR, INGROUND>::PreComputePotentialTerms( );
+
+    template<>
+    void KernelEM1DReflSpec<TE, INAIR, INGROUND>::PreComputePotentialTerms( );
+
+    ///////////////////////////////////////////////
+    // Default mode definitions
+
+/*
+    template<EMMODE Mode, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
+    void KernelEM1DReflSpec<Mode, Isource, Irecv>::SetTCache(const Real& rho0) {
+       #ifdef LEMMAUSEOMP
+        #pragma omp critical
+        #endif
+        {
+        this->tcache = &this->CACHE[rho0];
+        }
+    }
+*/
+
+/*
+    template<EMMODE Mode, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
+    void KernelEM1DReflSpec<Mode, Isource, Irecv>::ComputeReflectionCoeffs(const Real& lambda, const int& idx) {
+
+        if ( (std::abs(this->tcache->lambda[idx]-lambda) <= this->tcache->epsilon) &&
+            this->tcache->u[idx].size() > 0  && std::abs(this->kk(0) - this->tcache->kk[idx](0)) <= this->tcache->epsilon ) {
+            //std::cout << "USING CACHED RESULTS !!!!!!" << std::endl;
+            // load all the values we need
+            this->u   = this->tcache->u[idx];
+            this->rams = this->tcache->rams[idx];
+            this->cf = this->tcache->cf[idx];
+            //this->kk = this->tcache->kk[idx];
+            this->uk = this->tcache->uk[idx];
+            this->um = this->tcache->um[idx];
+            this->rtd = this->tcache->Rtd[idx];
+            this->rtu = this->tcache->Rtu[idx];
+
+        } else { // else do the work
+        }
+
+        ComputeReflectionCoeffs(lambda);
+
+        //#pragma omp critical
+        //{
+        //std::cout << idx << "\t" << lambda << "\t" << rtd.transpose() << std::endl;
+        //}
+        // store the results
+        this->tcache->u[idx]      = this->u;
+        this->tcache->cf[idx]     = this->cf;
+        this->tcache->kk[idx]     = this->kk;
+        this->tcache->uk[idx]     = this->uk;
+        this->tcache->um[idx]     = this->um;
+        this->tcache->Rtd[idx]    = this->rtd;
+        this->tcache->Rtu[idx]    = this->rtu;
+        this->tcache->zh0i[idx]    = std::imag(this->zh[0]);
+        this->tcache->lambda[idx] = lambda;
+        this->tcache->rams[idx]   = rams;
+
+        }
+
+        return;
+    }
+*/
+
+    template<EMMODE Mode, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
+    void KernelEM1DReflSpec<Mode, Isource, Irecv>::ComputeReflectionCoeffs(const Real& lambda) {
+        static bool called = false;
+        if (!called) {
+            std::cout << "unspecialised Reflection function KernelEM1DReflSpec<"
+                      << Mode << ", " << Isource << ", "
+                      << Irecv << " >::ComputeReflectionCoeffs( const Real& lambda ) --> SLOW PERFORMANCE EXPECTED\n";
+            called = true;
+        }
+
+        rams = lambda*lambda;
+        //////////////////////////////////////////
+        // Compute TEM stuff
+
+        // This call to sqrt takes ~ 15% of execution time
+        u  = (rams-kk.array()).sqrt();
+        uk = u(lays);
+        um = u(layr);
+
+        switch (Mode) {
+
+            // TM mode
+            case (TM):
+                Zyu(1) = -u(0)/yh(0);
+                Zyi    =  u.array() / yh.array();
+                break;
+
+            // TE mode
+            case (TE):
+                Zyu(1) = -u(0)/zh(0);
+                Zyi    =  u.array() / zh.array();
+                break;
+
+            default:
+                throw 11; //IllegalMode(this);
+        }
+
+        Zyd.tail<1>() = Zyi.tail<1>();
+
+        for (int ilay=1; ilay<nlay-1; ++ilay) {
+            cf(ilay) =
+                std::exp(-(Real)(2.)*u(ilay)*LayerThickness(ilay));
+            th(ilay) = ((Real)(1.)-cf(ilay)) / ((Real)(1.)+cf(ilay));
+        }
+
+        // Can't use blocks, b/c recursive
+        for (int N=1; N<lays; ++N){
+            Zyu(N+1)=Zyi(N)*(Zyu(N)-Zyi(N)*th(N)) /
+                            (Zyi(N)-Zyu(N)*th(N)) ;
+        }
+
+        int ne = nlay-2;
+        for (int N=ne; N >=lays+1; --N) {
+            Zyd(N) = Zyi(N)*(Zyd(N+1)+Zyi(N)*th(N)) /
+                            (Zyi(N)+Zyd(N+1)*th(N)) ;
+        }
+
+        rtd(nlay-1) = 0;
+
+        if (layr < lays) {
+            // Receiver above source layer
+            int ls = layr;
+            if (ls == 0) {
+                ls = layr+1;
+            }
+            for (int N=ls; N<=lays; ++N) {
+                rtu(N)= (Zyi(N)+Zyu(N)) /
+                        (Zyi(N)-Zyu(N)) ;
+            }
+            if (lays < nlay-1) {
+                rtd(lays) = (Zyi(lays)-Zyd(lays+1)) /
+                            (Zyi(lays)+Zyd(lays+1)) ;
+            }
+        } else {
+            // RECEIVER IN OR BELOW THE SOURCE LAYER
+            if (lays == layr) {  // Rx In source Layer
+                if (layr == 0) {
+                    rtd(0) = (Zyu(1)+Zyd(1)) /
+                             (Zyu(1)-Zyd(1)) ;
+                } else if (layr == nlay-1) {
+                    rtu(nlay-1) = (Zyi(nlay-1)+Zyu(nlay-1)) /
+                                  (Zyi(nlay-1)-Zyu(nlay-1)) ;
+                } else {
+                    rtu(layr) = (Zyi(layr)+Zyu(layr)) /
+                                (Zyi(layr)-Zyu(layr)) ;
+                    rtd(layr) = (Zyi(layr)-Zyd(layr+1)) /
+                                (Zyi(layr)+Zyd(layr+1)) ;
+                }
+            } else { // receiver below source layer
+                if (lays == 0) {
+                    rtd(0) = (Zyu(1)+Zyd(1)) /
+                             (Zyu(1)-Zyd(1)) ;
+                } else {
+                    rtu(lays) = (Zyi(lays)+Zyu(lays)) /
+                                (Zyi(lays)-Zyu(lays)) ;
+                }
+                int le = layr;
+                if (le == nlay-1) --le;
+                int ls = lays;
+                if (lays == 0   ) ++ls;
+
+                // TODO use blocks to vectorize maybe?
+                // This works but gives same to slightly worse
+                // performance as loop.
+//                 int nn = le-ls+1;
+//                 rtd.segment(ls, nn) =
+//                      (Zyi.segment(ls  , nn).array() -
+//                       Zyd.segment(ls+1, nn).array()).array() /
+//                      (Zyi.segment(ls  , nn).array() +
+//                       Zyd.segment(ls+1, nn).array()).array() ;
+                for (int N=ls; N<=le; ++N) {
+                    rtd(N) = (Zyi(N)-Zyd(N+1)) /
+                             (Zyi(N)+Zyd(N+1)) ;
+                }
+            }
+        } // End in or below source layer
+        return;
+    }
+
+    template<EMMODE Mode, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
+    void KernelEM1DReflSpec<Mode, Isource, Irecv>::PreComputePotentialTerms( ) {
+        static bool called = false;
+        if (!called) {
+            std::cerr << "unspecialised function KernelEM1DReflSpec<"
+                      << Mode << ", " << Isource << ", "
+                      << Irecv << " >::PreComputePotentialTerms\n";
+            called = true;
+        }
+    }
+
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef KERNELEM1DREFLSPEC_INC  -----

Modules/FDEM1D/include/layeredearthem.h

@@ -0,0 +1,314 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     06/24/2009
+  @version   0.0
+ **/
+
+#ifndef __LAYEREDEARTHEM_H
+#define __LAYEREDEARTHEM_H
+
+#include "layeredearth.h"
+#include <iomanip>
+
+namespace Lemma {
+
+    // =======================================================================
+    //        Class:  LayeredEarthEM
+    /// \brief  1D layered earth. Attributes include all aspects of
+    /// Cole-Cole model.
+    /// \details   Primarily used for EM calculations.
+    // =======================================================================
+    class LayeredEarthEM : public LayeredEarth {
+
+        public:
+
+            // ====================    FRIENDS     ===========================
+
+            /** Recursively streams information about this class */
+            friend std::ostream &operator<<(std::ostream &stream,
+                        const LayeredEarthEM &ob);
+
+            // ====================  LIFECYCLE     ===========================
+
+            /**
+             *  Public constructor. Creates a new instance of the class and
+             *  assigns a reference to the thrown pointer.
+             */
+            static LayeredEarthEM* New();
+
+            /**
+             * @copybrief LemmaObject::Delete()
+             * @copydetails LemmaObject::Delete()
+             */
+            void Delete();
+
+            #ifdef HAVE_YAMLCPP
+            /** YAML Serializing method
+             */
+            YAML::Node Serialize() const;
+
+
+            //static LayeredEarthEM* DeSerialize(const YAML::Node& node);
+            #endif
+
+            /** @return a deep copy
+             */
+			LayeredEarthEM* Clone();
+
+            // ====================  OPERATORS     ===========================
+
+            // ====================  OPERATIONS    ===========================
+
+            /** Evaluates the cole-cole model for suceptability and
+             * permeability.
+             * @param[in] omega is the frequency in Hz
+             */
+            void EvaluateColeColeModel(const Real& omega);
+
+            // ====================  ACCESS        ===========================
+
+            /** Sets the number of layers and resizes all model parameters to
+             *  be the correct size, finally initialises all values to free
+             *  space.
+             *  @param[in] nlay is the number of layers
+             */
+            virtual void SetNumberOfLayers(const int& nlay);
+
+            /** Sets Complex Conductivity of the layers
+             *  @param[in] sigma is a vector of the conducivity of the layers
+             */
+            void SetLayerConductivity(const VectorXcr &sigma);
+
+            /** Sets Complex Conductivity of a single layer
+             *  @param[in] sigma is  the conducivity of the layer
+             *  @param[in] ilay is  the layer index
+             */
+            void SetLayerConductivity(const int& ilay, const Complex &sigma);
+
+            /* Sets Complex resitivity of the layers
+             *  @param[in] ohm is a vector of the resistivity of the layers
+                Singularity at 0 resistivity in air. Need to reformaulat things a bit
+             */
+            //void SetLayerResistivity(const VectorXcr &ohm);
+
+            /** Sets the thickness of the layers
+             *  @param[in] thick is a vector of the thicknesses of the layers.
+             *  Must be two less than the total number of Layers as the top and
+             *  bottom layers are assumed infinite.
+             */
+            void SetLayerThickness(const VectorXr &thick);
+
+            /** Sets the High frequency susceptibility
+             */
+            void SetLayerHighFreqSusceptibility(const VectorXr& sushi);
+
+            /** Sets the Low frequency susceptibility
+             */
+            void SetLayerLowFreqSusceptibility(const VectorXr& sushi);
+
+            /** Sets the Layer breath susceptibility
+             */
+            void SetLayerBreathSusceptibility(const VectorXr& susbr);
+
+            /** Sets the Layer tau susceptibility
+             */
+            void SetLayerTauSusceptibility(const VectorXr& susta);
+
+            /** Sets the High frequency permitivity
+             */
+            void SetLayerHighFreqPermitivity(const VectorXr& sushi);
+
+            /** Sets the Low frequency permitivity
+             */
+            void SetLayerLowFreqPermitivity(const VectorXr& sushi);
+
+            /** Sets the Layer breath permitivity
+             */
+            void SetLayerBreathPermitivity(const VectorXr& oerbr);
+
+            /** Sets the Layer breath permitivity
+             */
+            void SetLayerTauPermitivity(const VectorXr& oerbr);
+
+            // ====================  INQUIRY       ===========================
+
+            /** Returns the thickness of a layer
+                @return a VectorXcr of the layer conductivities.
+             */
+            VectorXcr GetLayerConductivity( );
+
+            /** Returns the conductivity of a layer
+             *  @param[in] ilay is the layer indice of interest
+             *  @return the complex valued conductivity of the layer of
+             *  interest.
+             */
+            Complex GetLayerConductivity(const int &ilay);
+
+            /** Returns the susceptibility of a layer
+             *  @param[in] ilay is the layer indice of interest.
+             *  @return a Complex value of the electrical susceptibility of the
+             *  probes layer.
+             */
+            Complex GetLayerSusceptibility(const int &ilay);
+
+            /** Returns the Susceptibility of Cole-Cole model
+             *  @return a VectorXcr of the suceptibilities of the model.
+             */
+            VectorXcr GetLayerSusceptibility( );
+
+            /** Returns the low freq susceptibility of a layer
+             */
+            Real GetLayerLowFreqSusceptibility(const int &ilay);
+
+            /** Returns the low freq susceptibility of a layer
+             */
+            VectorXr GetLayerLowFreqSusceptibility( );
+
+            /** Returns the low freq susceptibility of a layer
+             */
+            Real GetLayerHighFreqSusceptibility(const int &ilay);
+
+            /** Returns the low freq susceptibility of a layer
+             */
+            VectorXr GetLayerHighFreqSusceptibility( );
+
+            /** Returns the low freq susceptibility of a layer
+             */
+            Real GetLayerTauSusceptibility(const int &ilay);
+
+            /** Returns the low freq susceptibility of a layer
+             */
+            VectorXr GetLayerTauSusceptibility( );
+
+            /** Returns the low freq susceptibility of a layer
+             */
+            Real GetLayerBreathSusceptibility(const int &ilay);
+
+            /** Returns the low freq susceptibility of a layer
+             */
+            VectorXr GetLayerBreathSusceptibility( );
+
+            /** Returns the Relative Permitivity of the cole cole model
+             */
+            VectorXcr GetLayerPermitivity( );
+
+            /** Returns the conductivity of a layer
+             *  @param[in] ilay is the layer indice of interest.
+             *  @return a Complex value of the electrical permitivity of the
+             *  probed layer.
+             */
+            Complex GetLayerPermitivity(const int &ilay);
+
+            /** Low Freq permivitity
+             */
+            VectorXr  GetLayerLowFreqPermitivity( );
+
+            /** Returns the low freq susceptibility of a layer
+             */
+            Real GetLayerLowFreqPermitivity(const int &ilay);
+
+            /** Returns the low freq susceptibility of a layer
+             */
+            Real GetLayerHighFreqPermitivity(const int &ilay);
+
+            /** Returns the low freq susceptibility of a layer
+             */
+            VectorXr GetLayerHighFreqPermitivity( );
+
+            /** Returns the low freq susceptibility of a layer
+             */
+            Real GetLayerTauPermitivity(const int &ilay);
+
+            /** Returns the low freq susceptibility of a layer
+             */
+            VectorXr GetLayerTauPermitivity( );
+
+            /** Returns the low freq susceptibility of a layer
+             */
+            Real GetLayerBreathPermitivity(const int &ilay);
+
+            /** Returns the low freq susceptibility of a layer
+             */
+            VectorXr GetLayerBreathPermitivity( );
+
+        protected:
+
+            // ====================  LIFECYCLE     ===========================
+
+            /** Default protected constructor. */
+            LayeredEarthEM (const std::string &name);
+
+            #ifdef HAVE_YAMLCPP
+            /** Default protected constructor. */
+			LayeredEarthEM (const YAML::Node& node);
+            #endif
+
+            /** Default protected constructor. */
+            ~LayeredEarthEM ();
+
+            /**
+             * @copybrief LemmaObject::Release()
+             * @copydetails LemmaObject::Release()
+             */
+            void Release();
+
+            // ====================  DATA MEMBERS  ===========================
+
+            /** Vector of layer Conductivity */
+            VectorXcr         LayerConductivity;
+
+            /** Vector of layer Susceptibility (chi)
+             *  This is calculated using the Cole-Cole model
+             *  \f[ sus(i) = sush(i)
+             *   + \frac{(susl(i)-sush(i))}  {(1+(jw * sustau(i))^{susalp(i)})} \f]
+             */
+            VectorXcr         LayerSusceptibility;
+
+            /** Vector of low frequency susceptibility, for use in Cole-Cole
+              model */
+            VectorXr          LayerLowFreqSusceptibility;
+
+            /** Vector of high frequency susceptibility, for use in Cole-Cole
+             model */
+            VectorXr          LayerHighFreqSusceptibility;
+
+            /** Vector of relaxation time constants, for use in Cole-Cole model
+             */
+            VectorXr          LayerTauSusceptibility;
+
+            /** Vector relaxation breath, for use in Cole-Cole model
+             */
+            VectorXr          LayerBreathSusceptibility;
+
+            /** Vector of Layer Permitivity (epsilon)
+             *  Calculated using the Cole-Cole model
+             *  \f[ epr(i) = eprh(i)
+             *     + \frac{ (eprl(i)-eprh(i))}  { (1+(jw*eprtau(i))^{epralp(i)})} \f]
+             */
+            VectorXcr         LayerPermitivity;
+
+            /** Low frequency permitivity for each layer */
+            VectorXr          LayerLowFreqPermitivity;
+
+            /** High frequency permitivity for each layer */
+            VectorXr          LayerHighFreqPermitivity;
+
+            /** Decay time constant for each layer */
+            VectorXr          LayerTauPermitivity;
+
+            /** Relaxation breath for each layer */
+            VectorXr          LayerBreathPermitivity;
+
+    }; // -----  end of class  LayeredEarthEM  -----
+
+
+} // namespace Lemma
+
+#endif // __LAYEREDEARTHEM_H

Modules/FDEM1D/include/modelreaderfem1d.h

@@ -0,0 +1,68 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   M. Andy Kass
+  @date     01/03/2013
+  @version  $Id$
+ **/
+
+#ifndef __MODELREADERFEM1D_H
+#define __MODELREADERFEM1D_H
+
+#include "modelreader.h"
+
+namespace Lemma {
+
+
+// ===================================================================
+//        Class:  ModelReaderFem1D
+/// \brief
+/// \details
+// ===================================================================
+	class ModelReaderFem1D : public ModelReader {
+
+		friend std::ostream &operator<<(std::ostream &stream,
+			const ModelReaderFem1D &ob);
+
+	public:
+
+	// ====================  LIFECYCLE     =======================
+
+	static ModelReaderFem1D* New();
+
+	void Delete();
+
+	// ====================  OPERATORS     =======================
+
+	// ====================  OPERATIONS    =======================
+
+	// ====================  ACCESS        =======================
+
+	// ====================  INQUIRY       =======================
+
+
+
+	protected:
+
+	// ====================  LIFECYCLE     =======================
+
+	/// Default protected constructor.
+	ModelReaderFem1D (const std::string &name);
+
+	/// Default protected constructor.
+	~ModelReaderFem1D ();
+
+	void Release();
+
+	// ====================  DATA MEMBERS  =========================
+
+	private:
+
+}; // -----  end of class  ModelReaderFem1D  -----
+} // end of namespace Lemma
+#endif // __MODELREADERFEM1D_H

Modules/FDEM1D/include/octreegrid.h

@@ -0,0 +1,358 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     03/19/2010
+  @version  $Id: octreegrid.h 193 2014-11-10 23:51:41Z tirons $
+ **/
+
+#ifndef  OCTREEGRID_INC
+#define  OCTREEGRID_INC
+
+// This class depends on VTK!
+
+#ifdef  LEMMAUSEVTK
+#include "grid.h"
+#include "vtkHyperOctree.h"        // In Filtering
+#include "vtkHyperOctreeCursor.h"
+#include "vtkHyperOctreeSampleFunction.h"
+#include "vtkImplicitFunction.h"
+#include "vtkCell.h"
+#include "vtkGenericCell.h"
+
+#ifdef  LEMMA_SINGLE_PRECISION
+#include "vtkFloatArray.h"
+#else      // -----  not LEMMA_SINGLE_PRECISION  -----
+#include "vtkDoubleArray.h"
+#endif     // -----  not LEMMA_SINGLE_PRECISION  -----
+
+#include "kernel.h"
+#include "receiverpoints.h"
+#include "receivercubes.h"
+#include "layeredearth.h"
+//#include "layeredearthnmr.h"
+#include "inversesolver.h"
+
+//#include "FastDelegate.h"
+//#include "FastDelegateBind.h"
+
+namespace Lemma {
+
+    // forward declaration
+    class InverseSolver ;
+
+    // ===================================================================
+    //        Class:  OctreeGrid
+    /** An Octree class, builds off VtkHyperOctree so this class can
+        only be used when compiled with VTK libs.
+        An Octree is a heirarchial 3D mesh with rectangular cells containing
+        either 0 or 8 children.
+     */
+    // ===================================================================
+    class OctreeGrid : public Grid {
+
+        friend class InverseSolver;
+        //friend class SNMRInversion1D;        // From Merlin Module
+
+        friend std::ostream &operator<<(std::ostream &stream,
+                const OctreeGrid &ob);
+
+        public:
+
+            // ====================  LIFECYCLE     =======================
+
+            /**
+             * new grid octreee
+             */
+            static OctreeGrid* New();
+
+            /**
+             * @copybrief LemmaObject::Delete()
+             * @copydetails LemmaObject::Delete()
+             */
+            void Delete();
+
+            // ====================  OPERATORS     =======================
+
+
+            // ====================  ACCESS        =======================
+
+            /** Sets the kernel function to be used to make the mesh.
+             *  @param[in] kern is a kernel that is used to generate a mesh.
+             */
+            void SetKernel(Kernel* kern);
+
+            /// Sets a 1D model associated with this kernel.
+            /// @param[in] model1d is a pointer to a LayeredEarth model that
+            /// will be used to pre-subdivide leaves that overlap several
+            /// layers.
+            void SetLayeredEarth(LayeredEarth* model1d);
+
+            /** Sets the size of the mesh
+                @param[in] size is the size of the mesh. The mesh must start at
+                [0,0,0] and goes to [sizex, sizey, sizez].
+             */
+            void SetSize(const Vector3r& size);
+
+            /** Sets the origin of the mesh
+                @param[in] origin is the origin of the mesh.
+             */
+            void SetOrigin(const Vector3r& origin);
+
+            /** Sets the minimum depth to model. This must be greater than 0.
+                @param[in] depth is the new minimum depth.
+             */
+            void SetMinimumDepth(const Real& depth);
+
+            /** Fills in the leaf data with the kernel sensitivity
+             */
+            void FillMeshWithKernel();
+
+            /** Fills in the leaf data with the kernel sensitivity
+             */
+            void FillMeshWithKernel(vtkImplicitFunction* Impl);
+
+            /** Sets the size of the mesh
+             */
+            void SetSize(const Real &x, const Real &y, const Real &z);
+
+            /** Generates mesh to specified tolerance.
+             *  @param[in] tol is the kernel tolerance.
+             */
+            void GenerateMesh(const Real &tol);
+
+
+            /** Generates a mesh to specified tolerance, but initially splits
+             *  based on implicit function.
+             *  @param[in] tol is the kernel tolerance.
+             *  @param[in] Impl is the implicit dataset used for initial
+             *  subdivision
+             *  @param[in] impltol is the tolerance for the initial model based
+             *  subdividing.
+             */
+            void GenerateMesh(const Real& tol, vtkImplicitFunction* Impl,
+                              const Real& impltol);
+
+            /** Generates an Octree mesh using a pre-sampled input Octree Dataset.
+                Speeds up repeated kernel calculations when the underlying model in
+                the above ImplicitFunction needs to be called often or is complex.
+             */
+            void GenerateMesh(const Real& tol, vtkImplicitFunction* Impl,
+                    vtkHyperOctreeSampleFunction* OctSamp);
+
+            /** Evaluates the kernel on the mesh. In some cases this is the same thing
+                as generate mesh, but if more that one calculation are needed on a
+                mesh you can use this method. It interfaces with the kernels by
+                calling
+             */
+            Complex EvaluateKernelOnMesh();
+
+            /** Returns a receiver cube class that represents the same Geometry as the
+                HyperOctree. This is useful as it can be passed directly to em1dearth,
+                and currently, an Octree cannot. But this requires storage of all the
+                cell volumes and locations. In the future, you should be able to pass
+                around this class just like a ReceiverCubes.
+             */
+            void ReceiverCubeRepresentation();
+
+            /** Returns the receiver cube class. */
+            ReceiverCubes* GetReceiverCubes();
+
+            /** returns the kernel sum from generation */
+            Complex GetKernelSum();
+
+            /** Accessor to underlying vtkClass.
+             *  @return a vtkHyperOctree that can be used for visualization.
+             */
+            vtkHyperOctree* GetVtkHyperOctree( );
+
+            /** Traverse the data structure and call a function at each leaf
+             */
+            void TraverseAndCall(InverseSolver* Inverse);
+
+            /** Traverse the data structure and call a function at each leaf
+             */
+            void TraverseAndCall( vtkImplicitFunction* Impl );
+
+            /**
+             */
+            void TraverseLeaves(vtkImplicitFunction* Impl);
+
+            /**
+             */
+            void FollowExistingTree(vtkHyperOctree* Leader, vtkHyperOctreeCursor* LeaderCursor,
+                    vtkImplicitFunction* Impl);
+
+            // ====================  OPERATIONS    =======================
+
+            /** Binds any derived member function of a derived class of
+                LayeredEarth to SampleScalarFromLayeredEarthFD. This function is then
+                used to sample the Octree mesh for that parameter. The member function
+                needs to be of the type GetLayerXXX(const int Layer& lay).
+                @param[in] earth is a pointer to a derived class of LayeredEarth
+                @param[in] fcnptr is a function pointer to a member function. It
+                should be called like &LayeredEarthNMR::GetLayerPorosity
+                @param[in] name is a std::string identifier.
+             */
+            template <class Derived>
+            void SampleScalarFromLayeredEarth(LayeredEarth* earth,
+                    Real (Derived::*fcnptr)(const int& id), const std::string &name) {
+                std::cerr << "In octreegrid.h SampleScalrFromLayeredEarth FastDelegate method was "
+                         << "removed, need to fix with move semantics or function pointer." << std::endl;
+                exit(3);
+                //TODO fix SampleScalar below, as call to SampleScalarFromLayeredEarthFD is
+                //     removed there.
+/*
+                SampleScalarFromLayeredEarthFD.bind(static_cast<Derived*>(earth), fcnptr);
+                GetLayerInt.bind(earth, &LayeredEarth::GetLayerAtThisDepth);
+                // TODO, don't use KernelArray, instead create new Array, and set it
+                // in there. Then delete?
+                this->KernelArray->SetName(name.c_str());
+                this->KernelArray->SetNumberOfTuples(Octree->GetNumberOfLeaves());
+                SampleScalar();
+                this->Octree->GetLeafData()->SetScalars( KernelArray );
+                this->Octree->GetLeafData()->AddArray( KernelArray );
+*/
+            }
+
+            /** Sends cursor to root
+             */
+            void CursorToRoot();
+
+            // ====================  INQUIRY       =======================
+
+        protected:
+
+            // ====================  LIFECYCLE     =======================
+
+            /** Default protected constructor. */
+            OctreeGrid (const std::string &name);
+
+            /** Default protected constructor. */
+            ~OctreeGrid ();
+
+            /**
+             * @copybrief LemmaObject::Release()
+             * @copydetails LemmaObject::Release()
+             */
+            void Release();
+
+            // ====================  OPERATIONS    =======================
+
+            /** Used internally. The leaf data is saved and then set as the vtk leaf
+             *  data.
+             */
+            void SetLeafDataFromGridCreation();
+
+            /** Return position of leaf, returns centre location
+             */
+            void GetPosition( Real* p );
+
+            /* Used to fill leaf data with a scalar value from a layered earth
+             *  model
+             */
+            //fastdelegate::FastDelegate1< const int&, Real > SampleScalarFromLayeredEarthFD;
+
+            /* Used to get the Layer of delagated model.
+             */
+            //fastdelegate::FastDelegate1< const Real&, int >  GetLayerInt;
+
+            /** Recursively determines the mesh to use
+             */
+            void EvaluateKids( );
+
+            /** Recursively determines the mesh to use
+                @param[in] kval is the current leaf kernel value
+                           which may be reused in analysis.
+             */
+            void EvaluateKids( Complex kval );
+
+            /** Same as above, but uses an implict function.
+             */
+            void EvaluateKids (vtkImplicitFunction* Impl);
+
+            /** Same as above, but lets function value be passed directly
+             */
+            void EvaluateKids (const Real& fval, vtkImplicitFunction* Impl);
+
+            /** Same as above but is passed a static fval to reuse. Useful when underlying model is smooth
+             */
+            void EvaluateKidsStatic(const Real& fval);
+
+            /** Same as above, but lets function value be passed directly
+             */
+            void SampleFunction(vtkImplicitFunction* Impl);
+
+            /** Recursively determines the mesh to use
+             */
+            void FillGrid( );
+
+            /** Recursively determines the mesh to use
+             */
+            void FillGrid(vtkImplicitFunction* Impl);
+
+            /** Used internally to build a receiver cube representation
+             */
+            void AssembleReceiverCubes( );
+
+            /** Samples a scalar from a LayeredEarth object. Used internally and calls
+             *  SampleScalarFromLayeredEarthFD, which can be set using
+             *  SampleScalarFromLayeredEarth.
+             */
+            void SampleScalar();
+
+
+
+            // Returns ReceiverPoints for the Octree.
+            //void ComputeFieldOnOctree( WireAntenna* loop );
+
+            // ====================  DATA MEMBERS  =========================
+
+        private:
+
+            Vector3r                Size;
+            Vector3r                Origin;
+            Vector3r                step;
+            Vector3r                cpos;
+
+            int                     level;
+            int                     maxlevel;
+            int                     index;
+            int                     counter;
+
+            Real                    cvol;
+            Real                    tvol;
+            Real                    tol;
+            Complex                 KernelSum;
+
+            Eigen::Matrix<Real, 8, 3> Posadd;
+
+            std::vector<Real>       leafdata;
+            std::vector<vtkIdType>  leafids;
+
+            Kernel                 *SenseKernel;
+            ReceiverCubes          *Cubes;
+            LayeredEarth           *Model1D;
+
+            vtkHyperOctree               *Octree;
+            vtkHyperOctreeCursor         *Cursor;
+            vtkHyperOctreeSampleFunction *OctSamp;
+
+            #ifdef  LEMMA_SINGLE_PRECISION
+            vtkFloatArray          *KernelArray;
+            #else      // -----  not LEMMA_SINGLE_PRECISION  -----
+            vtkDoubleArray         *KernelArray;
+            #endif     // -----  not LEMMA_SINGLE_PRECISION  -----
+            vtkDataArray           *SampleArray;
+
+    }; // -----  end of class  OctreeGrid  -----
+
+}       // -----  end of Lemma  name  -----
+
+#endif     // -----  not LEMMAUSEVTK  -----
+#endif   // ----- #ifndef OCTREEGRID_INC  -----

Modules/FDEM1D/include/receivercubes.h

@@ -0,0 +1,169 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     06/17/2010
+  @version  $Id: receivercubes.h 193 2014-11-10 23:51:41Z tirons $
+ **/
+
+#ifndef  RECEIVERCUBES_INC
+#define  RECEIVERCUBES_INC
+
+#include "receiverpoints.h"
+
+namespace Lemma {
+
+
+    // ===================================================================
+    //        Class:  ReceiverCubes
+    /** This class builds on Reciver points, but supports a cube around
+     * each point. It is a direct descendent and may be used wherever
+     * ReceiverPoints is used
+     */
+    // ===================================================================
+    class ReceiverCubes : public ReceiverPoints {
+
+        friend std::ostream &operator<<(std::ostream &stream,
+                const ReceiverCubes &ob);
+
+        friend class EmDipEarth1D;
+
+        public:
+
+            // ====================  LIFECYCLE     =======================
+
+            /**
+             *  Returns pointer to new DipoleSource. Location is
+             *  initialized to (0,0,0) type and polarization are
+             *  initialized  to nonworking values that will throw
+             *  exceptions if used.
+             */
+            static ReceiverCubes* New();
+
+            /**
+             * @copybrief LemmaObject::Delete()
+             * @copydetails LemmaObject::Delete()
+             */
+            void Delete();
+
+            // ====================  OPERATORS     =======================
+
+            // ====================  OPERATIONS    =======================
+
+            /** Sets the number of reciver cubes.
+             *  This method also resizes all the dynamic vectors in the class
+             *  to support this size.
+             *  @param[in] nrec is the number of cubes in the class.
+             */
+            void SetNumberOfReceivers(const int &nrec);
+
+            /** Sets the length of the x dimension of a single cube.
+             * @param[in] i is the cube number.
+             * @param[in] lx is the length of this cube, in this dimension.
+             */
+            void SetLengthX(const int &i, const Real &lx);
+
+            /** Sets the length of the y dimension of a single cube.
+             * @param[in] i is the cube number.
+             * @param[in] ly is the length of this cube, in this dimension.
+             */
+            void SetLengthY(const int &i, const Real &ly);
+
+            /** Sets the length of the z dimension of a single cube.
+             * @param[in] i is the cube number.
+             * @param[in] lz is the length of this cube, in this dimension.
+             */
+            void SetLengthZ(const int &i, const Real &lz);
+
+            /** Sets the lengths of all three dimensions of a single cube.
+             * @param[in] i is the cube number.
+             * @param[in] lx is the length of this cube, in this dimension.
+             * @param[in] ly is the length of this cube, in this dimension.
+             * @param[in] lz is the length of this cube, in this dimension.
+             */
+            void SetLength(const int &i, const Real& lx, const Real& ly,
+                            const Real &lz);
+
+            /** Sets the length of the x dimension of a single cube.
+             * @param[in] i is the cube number.
+             * @param[in] V is a vector of lenths.
+             */
+            void SetLength(const int &i, const Vector3r &V);
+
+
+            /** Gets the x dimension of cube i
+              * @param[in] i is the cube in quesion
+              * @return The legth of the x dimension of cube i
+              */
+            Real GetLengthX(const int &i);
+
+            /** Gets the y dimension of cube i
+              * @param[in] i is the cube in quesion
+              * @return The length of the y dimension of cube i
+              */
+            Real GetLengthY(const int &i);
+
+            /** Gets the z dimension of cube i
+              * @param[in] i is the cube in quesion
+              * @return The length of the z dimension of cube i
+              */
+            Real GetLengthZ(const int &i);
+
+            /** Gets the z dimension of cube i
+              * @param[in] i is the cube in quesion
+              * @return A vector of the lengths of the cube
+              */
+            Vector3r GetLength(const int& i);
+
+            /** Returns the volume of a cube
+              * @param[in] i is the cube of interest
+              * @return is the volume
+              */
+            Real GetVolume(const int&i);
+
+            /** Returns the volume of all the receiver cubes.
+              */
+            Real GetVolumeSum();
+
+            // ====================  ACCESS        =======================
+
+            // ====================  INQUIRY       =======================
+
+            // Returns the volume of a cube.
+            //Real GetCubeVolume(const int&i);
+            //VectorXr GetCubeVolumes();
+
+        protected:
+
+            // ====================  LIFECYCLE     =======================
+
+            /// Default protected constructor.
+            ReceiverCubes (const std::string &name);
+
+            /// Default protected constructor.
+            ~ReceiverCubes ();
+
+            /**
+             * @copybrief LemmaObject::Release()
+             * @copydetails LemmaObject::Release()
+             */
+            void Release();
+
+            // ====================  DATA MEMBERS  =========================
+
+            /// Dimension of each cube stored here, first indice is x, second y, and
+            /// third z
+            Vector3Xr Lengths;
+
+        private:
+
+    }; // -----  end of class  ReceiverCubes  -----
+
+}       // -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef RECEIVERCUBES_INC  -----

Modules/FDEM1D/include/receiverpoints.h

@@ -0,0 +1,281 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     12/02/2009
+  @version  $Id: receiverpoints.h 199 2014-12-29 19:25:20Z tirons $
+ **/
+
+#ifndef __RECEIVERPOINTS_H
+#define __RECEIVERPOINTS_H
+
+#ifdef LEMMAUSEVTK
+#include "vtkPointData.h"
+#include "vtkFieldData.h"
+#include "vtkGlyph3D.h"
+#include "vtkArrowSource.h"
+#include "vtkActor.h"
+#include "vtkPolyDataMapper.h"
+#include "vtkPoints.h"
+#include "vtkPolyData.h"
+#include "vtkDoubleArray.h"
+#include "vtkDataObject.h"
+#endif
+
+#include "LemmaObject.h"
+#include "dipolesource.h"
+
+#ifdef HAVE_YAMLCPP
+#include "yaml-cpp/yaml.h"
+#endif
+
+namespace Lemma {
+
+    // =======================================================================
+    //        Class:  ReceiverPoints
+    /// \brief  Points in the subsurface to make EM calculations,
+    ///  more general than the grids.
+    // =======================================================================
+    class ReceiverPoints : public LemmaObject {
+
+        public:
+
+            // ====================    FRIENDS     ===========================
+
+            /** Stream operator printing out information about this class.
+             */
+            friend std::ostream &operator<<(std::ostream &stream,
+                        const ReceiverPoints &ob);
+
+            friend class EMEarth1D;
+            friend class DipoleSource;
+
+            // ====================  LIFECYCLE     ===========================
+
+            /**
+             *  Returns pointer to new DipoleSource. Location is
+             *  initialized to (0,0,0) type and polarization are
+             *  initialized  to nonworking values that will throw
+             *  exceptions if used.
+             */
+            static ReceiverPoints* New();
+
+
+            /**
+             * @copybrief LemmaObject::Delete()
+             * @copydetails LemmaObject::Delete()
+             */
+            void Delete();
+
+            // ====================  OPERATORS     ===========================
+
+            // ====================  OPERATIONS    ===========================
+
+            // ====================  ACCESS        ===========================
+
+            /// Sets the number of receivers
+            virtual void SetNumberOfReceivers(const int &nrec);
+
+            /// Returns the location of a single receiver as an Eigen Vector
+            void SetLocation(const int& nrec, const Vector3r& loc);
+
+            /// Returns the location of a single receiver as an Eigen Vector
+            void SetLocation(const int& nrec, const Real& xp, const Real& yp,
+                            const Real& zp);
+
+            // ====================  INQUIRY       ===========================
+
+            /// Returns the number of receiverpoints.
+            int GetNumberOfReceivers();
+
+            /// Returns all the receiver locations as a 3 X matrix
+            Vector3Xr GetLocations();
+
+            /// Returns all the receiver locations as a general matrix, useful for python wrapper
+            MatrixXr GetLocationsMat();
+
+            /// Returns the E field for all locations
+            /// nfreq is the freqency desired
+            Vector3Xcr GetEfield(const int &nfreq);
+
+            /// Returns the E field for all locations
+            /// nfreq is the freqency desired, cast to general dynamic matrix, for python interoperability
+            MatrixXcr GetEfieldMat(const int &nfreq);
+
+            /// Returns the H field for all locations
+            /// nfreq is the freqency desired, cast to general dynamic matrix, for python interoperability
+            MatrixXcr GetHfieldMat(const int &nfreq);
+
+            /// Returns the H field for all locations
+            /// nfreq is the freqency desired
+            Vector3Xcr GetHfield(const int &nfreq);
+
+            /// Returns all of the computed H fields. Every frequency
+            std::vector<Vector3Xcr> GetHfield( );
+
+            /// Returns all of the computed E fields. Every frequency
+            std::vector<Vector3Xcr> GetEfield( );
+
+            /// Returns the E field of a single receiver as an Eigen Vector
+            /// nfreq is the freqency desired
+            Vector3cr GetEfield(const int &nfreq, const int& loc);
+
+            /// Returns the H field of a single receiver as an Eigen Vector
+            /// nfreq is the freqency desired
+            Vector3cr GetHfield(const int &nfreq, const int& loc);
+
+            /// Returns the B field of a single receiver as an Eigen Vector
+            /// nfreq is the freqency desired
+            Vector3cr GetBfield(const int &nfreq, const int& loc);
+
+            #ifdef LEMMAUSEVTK
+            /// Returns vtk Glyph actor that can be placed into scenes
+            vtkActor* GetVtkGlyphActor(const FIELDTYPE &ftype,
+                const Real& clip, const Real &scale,
+                const int &nfreq);
+
+            /// Returns a vtk Data Object that can easily be plotted
+            vtkDataObject * GetVtkDataObject(const FIELDTYPE &ftype,
+                const int& nbin,
+                const int& start, const int& end,
+                const FIELDCOMPONENT& fcomp,
+                const SPATIALCOORDINANT& scord);
+
+            /// Returns a vtk Data Object that can easily be plotted
+            vtkDataObject * GetVtkDataObjectFreq(const FIELDTYPE &ftype,
+                const int& nrec,
+                const int& fstart, const int& fend,
+                const FIELDCOMPONENT& fcomp,
+                const VectorXr& Freqs);
+            #endif
+
+            /// Returns the location of a single receiver as an Eigen Vector
+            Vector3r GetLocation(const int& loc);
+
+            /// Returns the x component of the location
+            Real GetLocationX(const int& loc);
+
+            /// Returns the y component of the location
+            Real GetLocationY(const int& loc);
+
+            /// Returns the z component of the location
+            Real GetLocationZ(const int& loc);
+
+            /// Resets fields
+            void ClearFields();
+
+            /// Sets the mask variable to true for this point.
+            void MaskPoint(const int& i);
+
+            /// Turns the mask off for this point.
+            void UnMaskPoint(const int& i);
+
+            /// Removes making on all points
+            void UnMaskAllPoints();
+
+            /// Returns the mask for this point
+            int GetMask(const int& i);
+
+            #ifdef HAVE_YAMLCPP
+        	/**
+             *  Uses YAML to serialize this object.
+             *  @return a YAML::Node
+             */
+            YAML::Node Serialize() const;
+
+            /**
+             *   Constructs an object from a YAML::Node.
+             */
+            static ReceiverPoints* DeSerialize(const YAML::Node& node);
+            #endif
+
+        protected:
+
+            // ====================  LIFECYCLE     ===========================
+
+            /// Default protected constructor.
+            ReceiverPoints (const std::string& name);
+
+            #ifdef HAVE_YAMLCPP
+            /// Default protected constructor.
+            ReceiverPoints (const YAML::Node& node);
+            #endif
+
+            /// Default protected constructor.
+            ~ReceiverPoints ();
+
+            /**
+             * @copybrief LemmaObject::Release()
+             * @copydetails LemmaObject::Release()
+             */
+            void Release();
+
+            // ====================  OPERATIONS    ===========================
+
+            /// Sets the number of H bins. These bins are often frequencies.
+            void SetNumberOfBinsH(const int& nbins);
+
+            /// Sets the number of E bins. These bins are often frequencies.
+            void SetNumberOfBinsE(const int& nbins);
+
+            /** Internal function that resizes the EField data structure */
+            void ResizeEField();
+
+            /** Internal function that resizes the HField data structure */
+            void ResizeHField();
+
+            /// Sets the value of the E field
+            void SetEfield(const int &nfreq, const int& loc,
+                const Complex &ex, const Complex &ey, const Complex &ez);
+
+            /// Sets the value of the H field
+            void SetHfield(const int &nfreq, const int& loc,
+                const Complex &hx, const Complex &hy, const Complex &hz);
+
+            /// Appends the value of the E field. This method is not
+            /// thread safe.
+            void AppendEfield(const int&nfreq, const int& loc,
+                const Complex &ex, const Complex &ey, const Complex &ez);
+
+            /// Appends the value of the H field. This method is not
+            /// thread safe.
+            void AppendHfield(const int &nfreq, const int& loc,
+                const Complex &hx, const Complex &hy, const Complex &hz);
+
+            // ====================  DATA MEMBERS  ===========================
+
+            /// Number of receivers
+            int                         NumberOfReceivers;
+
+            /// Number of fields
+            int                         NumberOfBinsE;
+
+            /// Number of fields
+            int                         NumberOfBinsH;
+
+            /// Used to mask this point so no computation is made at
+            /// this point.
+            VectorXi                    Mask;
+
+            /// Locations of receivers
+            Vector3Xr                   Locations;
+
+        private:
+
+            // NOTE, these are not serialized in output!
+
+            /// Electric field at receiver locations
+            std::vector<Vector3Xcr>     Efield;
+
+            /// H field at receiver locations
+            std::vector<Vector3Xcr>     Hfield;
+
+    }; // -----  end of class  ReceiverPoints  -----
+}
+
+#endif // __RECEIVERPOINTS

Modules/FDEM1D/include/sintransintegrationkernel.h

@@ -0,0 +1,97 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     02/08/2011
+  @version  $Id: sintransintegrationkernel.h 87 2013-09-05 22:44:05Z tirons $
+ **/
+
+#ifndef  SINTRANSINTEGRATIONKERNEL_INC
+#define  SINTRANSINTEGRATIONKERNEL_INC
+
+#include "integrationkernel.h"
+
+namespace Lemma {
+
+    // ===================================================================
+    //  Class:  SinTransIntegrationKernel
+    /**
+      @class
+      \brief    Integration kernel for testing sinine transform.
+      \details  Evaluates sinine at the argument, using lagged convolution.
+                all of these kernels have exact solutions.
+     */
+    // ===================================================================
+    class SinTransIntegrationKernel : public IntegrationKernel<Real> {
+
+        public:
+
+            // ====================  LIFECYCLE     =======================
+
+            /** Returns a pointer to a new object of type SinTransIntegrationKernel.
+             * It allocates all necessary memory.
+             */
+            static SinTransIntegrationKernel* New();
+
+            /** Deletes this object. Delete also disconnects any
+             * attachments to this object.
+             */
+            void Delete();
+
+            // ====================  OPERATORS     =======================
+
+            Real Argument(const Real&x, const int& iRelated);
+
+            int GetNumRel();
+
+            /// Sets the value 'A' used in test cases
+            void SetA(const Real& A);
+
+            /** Sets the integral to evaluate (1, 2, 3)
+             */
+            void SetIntegral(const int& i);
+
+            /** Returns the analytical answer at A and B */
+            Real GetAnalytical(const Real& B);
+            // ====================  OPERATIONS    =======================
+
+            // ====================  ACCESS        =======================
+
+            // ====================  INQUIRY       =======================
+
+        protected:
+
+            // ====================  LIFECYCLE     =======================
+
+            /** Deletes this object. Delete also disconnects any
+             * attachments to this object.
+             */
+            void Release();
+
+            /// Default protected constructor.
+            SinTransIntegrationKernel (const std::string& name);
+
+            /// Default protected constructor.
+            ~SinTransIntegrationKernel ();
+
+            // ====================  DATA MEMBERS  =========================
+
+            /** Value used in test cases  */
+            Real A;
+
+            /** Test integral to evaluate */
+            int Integral;
+
+        private:
+
+    }; // -----  end of class  SinTransIntegrationKernel  -----
+
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef SINTRANSINTEGRATIONKERNEL_INC  -----

Modules/FDEM1D/src/FHTKey.cpp

@@ -0,0 +1,359 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      02/11/2014 03:42:53 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#include "FHTKey.h"
+
+namespace Lemma {
+
+    // ====================  FRIEND METHODS  =====================
+
+    std::ostream &operator<<(std::ostream &stream, const FHTKey &ob) {
+
+        stream << *(HankelTransform*)(&ob);
+
+        return stream;
+    }
+
+
+    // ====================  STATIC CONST MEMBERS     ============
+
+    const Eigen::Matrix<Real, 201, 3>  FHTKey::WT201 =
+        ( Eigen::Matrix<Real, 201, 3>()   <<
+        // Base                   J0                      J1
+          4.1185887075357082e-06, 1.5020099209519960e-03, 4.7827871332506182e-10
+        , 4.6623077830484039e-06,-1.0381698214761684e-02,-2.9784175503440788e-09
+        , 5.2778064058937756e-06, 3.6840860097595164e-02, 9.7723832770897220e-09
+        , 5.9745606155328603e-06,-8.9903380392274704e-02,-2.2382340996085809e-08
+        , 6.7632974390298035e-06, 1.7082286536833860e-01, 4.0446774329470848e-08
+        , 7.6561600412698171e-06,-2.7115749656836280e-01,-6.1734815854553919e-08
+        , 8.6668946776271221e-06, 3.7649328091859574e-01, 8.3293912185608189e-08
+        , 9.8110623273521872e-06,-4.7220778569122657e-01,-1.0249453502284080e-07
+        , 1.1106278265924788e-05, 5.4778211089647089e-01, 1.1780779749909977e-07
+        , 1.2572483264760042e-05,-5.9823516853035097e-01,-1.2870061460834850e-07
+        , 1.4232250593579901e-05, 6.2345791612185331e-01, 1.3559243438349901e-07
+        , 1.6111133551969887e-05,-6.2650436648257724e-01,-1.3921010821521872e-07
+        , 1.8238058880617237e-05, 6.1197225351173345e-01, 1.4065745722769670e-07
+        , 2.0645772109076137e-05,-5.8470173866140451e-01,-1.4074881908375281e-07
+        , 2.3371341696506312e-05, 5.4911055789616858e-01, 1.4051720878600928e-07
+        , 2.6456729726989950e-05,-5.0878861684860843e-01,-1.4040746687777830e-07
+        , 2.9949437945688260e-05, 4.6652106345430200e-01, 1.4127886061686993e-07
+        , 3.3903239082024059e-05,-4.2426478870289325e-01,-1.4315595655055356e-07
+        , 3.8379004719130766e-05, 3.8339538911933357e-01, 1.4689283208027915e-07
+        , 4.3445642455208216e-05,-3.4472344791723936e-01,-1.5210916706348747e-07
+        , 4.9181156785051293e-05, 3.0876891466890510e-01, 1.5989801550138741e-07
+        , 5.5673850034776868e-05,-2.7570439368364807e-01,-1.6940918407911260e-07
+        , 6.3023681838995322e-05, 2.4562331000974616e-01, 1.8227089415749844e-07
+        , 7.1343808090545215e-05,-2.1839207265400126e-01,-1.9695856878603369e-07
+        , 8.0762323056016586e-05, 1.9393194321380827e-01, 2.1603952427106760e-07
+        , 9.1424231478173270e-05,-1.7198162962644575e-01,-2.3691320619292838e-07
+        , 1.0349368102719458e-04, 1.5242270280410272e-01, 2.6369843208466607e-07
+        , 1.1715648947091054e-04,-1.3494945901825492e-01,-2.9202021404039016e-07
+        , 1.3262300547161834e-04, 1.1946763189654602e-01, 3.2852445086324662e-07
+        , 1.5013134705348249e-04,-1.0565870880444576e-01,-3.6589094553627693e-07
+        , 1.6995106759902750e-04, 9.3482355548033913e-02, 4.1487501036863030e-07
+        , 1.9238730581535294e-04,-8.2612525279836244e-02,-4.6327136995173986e-07
+        , 2.1778548356175115e-04, 7.3077763526174969e-02, 5.2852697369750518e-07
+        , 2.4653662386513240e-04,-6.4536481281701225e-02,-5.9034983719954077e-07
+        , 2.7908337099788406e-04, 5.7096310621587334e-02, 6.7710211611560898e-07
+        , 3.1592680530155527e-04,-5.0384859605213800e-02,-7.5512942807901028e-07
+        , 3.5763415767542709e-04, 4.4599557396733047e-02, 8.7062473466409799e-07
+        , 4.0484754250000483e-04,-3.9316995063444334e-02,-9.6788530918130449e-07
+        , 4.5829384344501882e-04, 3.4838544754296139e-02, 1.1222658353725904e-06
+        , 5.1879590436097246e-04,-3.0664946477420088e-02,-1.2417228058919743e-06
+        , 5.8728519754599128e-04, 2.7221072240291456e-02, 1.4493467036899140e-06
+        , 6.6481616442494776e-04,-2.3901586108434601e-02,-1.5932456559208080e-06
+        , 7.5258244942583781e-04, 2.1281566646364738e-02, 1.8747045814274419e-06
+        , 8.5193527698548301e-04,-1.8612484595521447e-02,-2.0433320340041385e-06
+        , 9.6440425461164468e-04, 1.6655386303461400e-02, 2.4285695351967146e-06
+        , 1.0917209222795108e-03,-1.4472420076504743e-02,-2.6179926456520528e-06
+        , 1.2358454107222641e-03, 1.3057747649606617e-02, 3.1511729661391781e-06
+        , 1.3989966190390965e-03,-1.1226286001060300e-02,-3.3492412032881268e-06
+        , 1.5836863762264436e-03, 1.0266818557930830e-02, 4.0964186613549959e-06
+        , 1.7927581125735061e-03,-8.6738022421653585e-03,-4.2758275751239154e-06
+        , 2.0294306362957340e-03, 8.1103368670848164e-03, 5.3371197552207799e-06
+        , 2.2973476893787268e-03,-6.6573628142085938e-03,-5.4435423773626499e-06
+        , 2.6006340455800008e-03, 6.4551189810889585e-03, 6.9725766921672099e-06
+        , 2.9439590142573526e-03,-5.0524015117839084e-03,-6.9045562968161745e-06
+        , 3.3326083277104117e-03, 5.1989014270506263e-03, 9.1397025436977438e-06
+        , 3.7725655187922052e-03,-3.7597430078747883e-03,-8.7148373033635960e-06
+        , 4.2706040416570154e-03, 4.2640545165292636e-03, 1.2029590806160379e-05
+        , 4.8343915539089625e-03,-2.6994965688974474e-03,-1.0927976968519436e-05
+        , 5.4726079656493079e-03, 3.5928000560587229e-03, 1.5912526719455299e-05
+        , 6.1950790728715292e-03,-1.8061291289989019e-03,-1.3582559661331659e-05
+        , 7.0129278325854246e-03, 3.1436470898586703e-03, 2.1176226828087565e-05
+        , 7.9387456086585442e-03,-1.0244200001620755e-03,-1.6678205993448338e-05
+        , 8.9867860248264830e-03, 2.8888297674091743e-03, 2.8384979250408712e-05
+        , 1.0173184409377162e-02,-3.0605070741955765e-04,-2.0132088397797457e-05
+        , 1.1516206210016314e-02, 2.8125907445050334e-03, 3.8372045311188108e-05
+        , 1.3036528203437736e-02, 3.9337862066047565e-04,-2.3702184335455945e-05
+        , 1.4757556829019875e-02, 2.9102041487017727e-03, 5.2385308850007940e-05
+        , 1.6705788547622769e-02, 1.1170884769911178e-03,-2.6854373943701261e-05
+        , 1.8911217773465227e-02, 3.1876763415953362e-03, 7.2318581557902158e-05
+        , 2.1407798659484324e-02, 1.9097806429850762e-03,-2.8535361884516687e-05
+        , 2.4233967845691123e-02, 3.6621020321465411e-03, 1.0108123118106823e-04
+        , 2.7433236218606032e-02, 2.8203783587849949e-03,-2.6788477540644352e-05
+        , 3.1054858792331431e-02, 4.3626885599390430e-03, 1.4319185407094621e-04
+        , 3.5154593024557458e-02, 3.9050024915686802e-03,-1.8108424211338017e-05
+        , 3.9795557242315927e-02, 5.3324923486866077e-03, 2.0573561552327273e-04
+        , 4.5049202393557801e-02, 5.2303399394270488e-03, 3.6361648565843316e-06
+        , 5.0996412085361466e-02, 6.6309348458396984e-03, 2.9991264692859609e-04
+        , 5.7728747844643331e-02, 6.8775540687037451e-03, 4.8993332079278846e-05
+        , 6.5349858773045680e-02, 8.3371689988226087e-03, 4.4354733854670903e-04
+        , 7.3977077298642363e-02, 8.9468564745410102e-03, 1.3589101811995494e-04
+        , 8.3743225592195963e-02, 1.0554326601376745e-02, 6.6515823521273764e-04
+        , 9.4798660459030126e-02, 1.1562765604509096e-02, 2.9451991608624389e-04
+        , 1.0731358818908403e-01, 1.3414536265660639e-02, 1.0105553806271136e-03
+        , 1.2148068500391276e-01, 1.4879837399735491e-02, 5.7533964792254050e-04
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+        , 5.3794443759467447e-01, 6.1949790434151823e-02, 1.5745093424331037e-02
+        , 6.0896164107289685e-01, 6.8682064905571841e-02, 2.3708966370000140e-02
+        , 6.8935424252422239e-01, 7.5616743950118387e-02, 2.5740590762136872e-02
+        , 7.8035994327803426e-01, 8.2584983563572259e-02, 3.7232782843117498e-02
+        , 8.8337984088275090e-01, 8.9193635262987042e-02, 4.1225008900614292e-02
+        , 1.0000000000000000e+00, 9.4874686942005279e-02, 5.7507103212277359e-02
+        , 1.1320158709991752e+00, 9.8891681869094042e-02, 6.4044642846235691e-02
+        , 1.2814599321940212e+00, 1.0004294654495730e-01, 8.6091796551857253e-02
+        , 1.4506329812931589e+00, 9.7016844329802857e-02, 9.4717139804457451e-02
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+        , 3.4556134647626755e+00,-1.6020950407348281e-01, 7.7489831356083380e-02
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+        , 7.6707539338295589e+01,-8.6253791756068252e-04, 2.8918247156763971e-02
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+        , 1.2596448473034971e+02,-2.4698212240059978e-04, 1.6229579362363859e-02
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+        , 1.6141844006140866e+02,-1.5357911509105972e-04, 1.2396084121011890e-02
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+        , 1.9275402746900081e+03,-8.3853711343938338e-06, 9.5211407460757294e-04
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+        , 6.6608341270911405e+03,-2.4168587823583312e-06, 2.6581280850704716e-04
+        , 7.5401699459601114e+03, 2.1310948134441218e-06,-2.3378310479588391e-04
+        , 8.5355920488578286e+03,-1.8780185742021288e-06, 2.0554143583887405e-04
+        , 9.6624256676814348e+03, 1.6538488252707735e-06,-1.8063040107732216e-04
+        , 1.0938019208165191e+04,-1.4552318768651144e-06, 1.5864667598176302e-04
+        , 1.2382011340936813e+04, 1.2791890865306748e-06,-1.3923451235168759e-04
+        , 1.4016633352832258e+04,-1.1230741959148155e-06, 1.2208003098625932e-04
+        , 1.5867051413382505e+04, 9.8453630538596172e-07,-1.0690622166177854e-04
+        , 1.7961754025908867e+04,-8.6148574493190796e-07, 9.3468580362568137e-05
+        , 2.0332990628312182e+04, 7.5206242699701732e-07,-8.1551328581234316e-05
+        , 2.3017268096126892e+04,-6.5460810334682633e-07, 7.0964174631531072e-05
+        , 2.6055912791858576e+04, 5.6764451596029765e-07,-6.1539592468666665e-05
+        , 2.9495706813754354e+04,-4.8985884555184997e-07, 5.3130609116145443e-05
+        , 3.3389608239508460e+04, 4.2009674106879252e-07,-4.5609105983126460e-05
+        , 3.7797566453568354e+04,-3.5736212641225517e-07, 3.8864648584181207e-05
+        , 4.2787445110585410e+04, 3.0082215969939671e-07,-3.2803856352344075e-05
+        , 4.8436066944688770e+04,-2.4981510481639669e-07, 2.7350296775876261e-05
+        , 5.4830396510166145e+04, 2.0385823466866512e-07,-2.2444816150805301e-05
+        , 6.2068879062685897e+04,-1.6265189071584773e-07, 1.8046076281584239e-05
+        , 7.0262956194088882e+04, 1.2607416700611311e-07,-1.4130826937491561e-05
+        , 7.9538781555028458e+04,-9.4158417913450858e-08, 1.0693106849359383e-05
+        , 9.0039163080228551e+04, 6.7043911217063425e-08,-7.7412053314530284e-06
+        , 1.0192576161830177e+05,-4.4891090827293947e-08, 5.2910576443698300e-06
+        , 1.1538157981559623e+05, 2.7761325666544702e-08,-3.3552268362550323e-06
+        , 1.3061377957221285e+05,-1.5480404355710375e-08, 1.9282956206367452e-06
+        , 1.4785687144693290e+05, 7.5327300141098751e-09,-9.7253712572058755e-07
+        , 1.6737632511421290e+05,-3.0524770418657847e-09, 4.1100807632959352e-07
+        , 1.8947265645880660e+05, 9.5877856096830783e-10,-1.3553176263207053e-07
+        , 2.1448605423174356e+05,-2.0575286298055636e-10, 3.0748587523233524e-08
+        , 2.4280161749832361e+05, 2.2414416956474645e-11,-3.5668195345476294e-09 ).finished();
+
+    // ====================  LIFECYCLE     =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey
+    //      Method:  FHTKey
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    FHTKey::FHTKey (const std::string& name) : HankelTransform(name) {
+
+    }  // -----  end of method FHTKey::FHTKey  (constructor)  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey
+    //      Method:  New()
+    // Description:  public constructor
+    //--------------------------------------------------------------------------------------
+    FHTKey* FHTKey::New() {
+        FHTKey*  Obj = new FHTKey("FHTKey");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey
+    //      Method:  ~FHTKey
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    FHTKey::~FHTKey () {
+
+    }  // -----  end of method FHTKey::~FHTKey  (destructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey
+    //      Method:  Delete
+    // Description:  public destructor
+    //--------------------------------------------------------------------------------------
+    void FHTKey::Delete() {
+        this->DetachFrom(this);
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey
+    //      Method:  Release
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    void FHTKey::Release() {
+        delete this;
+    }
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey
+    //      Method:  Zgauss
+    //--------------------------------------------------------------------------------------
+    Complex FHTKey::Zgauss ( const int &ikk, const EMMODE &imode,
+                            const int &itype, const Real &rho,
+                            const Real &wavef, KernelEm1DBase *Kernel ) {
+ 		return Zans(0, Kernel->GetManagerIndex());
+    }		// -----  end of method FHTKey::ComputeRelated  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey
+    //      Method:  ComputeRelated
+    //--------------------------------------------------------------------------------------
+    void FHTKey::ComputeRelated ( const Real& rho, KernelEm1DBase* Kernel ) {
+        return ;
+    }		// -----  end of method FHTKey::ComputeRelated  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey
+    //      Method:  ComputeRelated
+    //--------------------------------------------------------------------------------------
+    void FHTKey::ComputeRelated ( const Real& rho, std::vector< KernelEm1DBase* > KernelVec ) {
+        return ;
+    }		// -----  end of method FHTKey::ComputeRelated  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey
+    //      Method:  ComputeRelated
+    //--------------------------------------------------------------------------------------
+    void FHTKey::ComputeRelated ( const Real& rho, KernelEM1DManager* KernelManager ) {
+
+        //kernelVec = KernelManager->GetSTLVector();
+        int nrel = (int)(KernelManager->GetSTLVector().size());
+        Eigen::Matrix<Complex, 201, Eigen::Dynamic > Zwork;
+        // TODO, if we want to allow lagged, then 1 below should be nlag
+        Zans= Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic>::Zero(1, nrel);
+        Zwork.resize(201, nrel);
+        VectorXr lambda = WT201.col(0).array()/rho;
+        int NumFun = 0;
+        int idx = 0;
+
+        // Get Kernel values
+        for (int ir=0; ir<lambda.size(); ++ir) {
+            // irelated loop
+            ++NumFun;
+            KernelManager->ComputeReflectionCoeffs(lambda(ir), idx, rho);
+            for (int ir2=0; ir2<nrel; ++ir2) {
+                // Zwork* needed due to sign convention of filter weights
+ 			    Zwork(ir, ir2) = std::conj(KernelManager->GetSTLVector()[ir2]->RelBesselArg(lambda(ir)));
+            }
+
+        }
+
+        // We diverge slightly from Key here, each kernel is evaluated seperately, whereby instead
+        // they prefer to sum them. The reason is that all those terms have been removed from the kernels
+        // in the interests of making them as generic and reusable as possible. This approach requires slightly
+        // more multiplies, but the same number of kernel evaluations, which is the expensive part.
+        // Inner product and scale
+        for (int ir2=0; ir2<nrel; ++ir2) {
+            Zans(0, ir2) = Zwork.col(ir2).dot(WT201.col(KernelManager->GetSTLVector()[ir2]->GetBesselOrder() + 1))/rho;
+        }
+
+        return ;
+    }		// -----  end of method FHTKey::ComputeRelated  -----
+
+}		// -----  end of Lemma  name  -----

Modules/FDEM1D/src/FHTKey101.cpp

@@ -0,0 +1,259 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      02/11/2014 03:42:53 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#include "FHTKey101.h"
+
+namespace Lemma {
+
+    // ====================  FRIEND METHODS  =====================
+
+    std::ostream &operator<<(std::ostream &stream, const FHTKey101 &ob) {
+
+        stream << *(HankelTransform*)(&ob);
+
+        return stream;
+    }
+
+
+    // ====================  STATIC CONST MEMBERS     ============
+
+    const Eigen::Matrix<Real, 101, 3>  FHTKey101::WT101 =
+        ( Eigen::Matrix<Real, 101, 3>()   <<
+       // Base                   J0                      J1
+       5.5308437014783363e-04,   5.1818808036862153e-02,   4.1746363961646286e-06,
+       6.4259236035555788e-04,  -2.9258492652779172e-01,  -2.5993370843637242e-05,
+       7.4658580837667996e-04,   8.7289913080159265e-01,   9.2506838353721647e-05,
+       8.6740895730700251e-04,  -1.8525183961240297e+00,  -2.4318740269846489e-04,
+       1.0077854290485113e-03,   3.2096055660873608e+00,   5.2276050788732404e-04,
+       1.1708796207911744e-03,  -4.9248158048315069e+00,  -9.5803859755432658e-04,
+       1.3603680375478939e-03,   7.0219167445719828e+00,   1.5308357107396591e-03,
+       1.5805221687362171e-03,  -9.4781099645811544e+00,  -2.1584605764249656e-03,
+       1.8363047770289071e-03,   1.2098564895534539e+01,   2.7161344302423967e-03,
+       2.1334817700377098e-03,  -1.4476661837664896e+01,  -3.0845361397036195e-03,
+       2.4787521766663585e-03,   1.6146079632847474e+01,   3.2133980102756368e-03,
+       2.8798991580882430e-03,  -1.6810370923047440e+01,  -3.1305779240645847e-03,
+       3.3459654574712720e-03,   1.6506202923977266e+01,   2.9239120736637542e-03,
+       3.8874572434761303e-03,  -1.5534747212675301e+01,  -2.6680602560576316e-03,
+       4.5165809426126703e-03,   1.4267433361428399e+01,   2.4131379039476304e-03,
+       5.2475183991813838e-03,  -1.2939053370802849e+01,  -2.1549566068119440e-03,
+       6.0967465655156379e-03,   1.1628520257389562e+01,   1.9058200916563901e-03,
+       7.0834089290521185e-03,  -1.0325503688577493e+01,  -1.6533122444456158e-03,
+       8.2297470490200302e-03,   9.0574401975545840e+00,   1.4391633836110848e-03,
+       9.5616019305435132e-03,  -7.8759096646654951e+00,  -1.2363666069459527e-03,
+       1.1108996538242306e-02,   6.8446506699312666e+00,   1.0907227256323094e-03,
+       1.2906812580479873e-02,  -5.9542991234257840e+00,  -9.2712769282234358e-04,
+       1.4995576820477703e-02,   5.1830565431894602e+00,   8.2888526218099687e-04,
+       1.7422374639493515e-02,  -4.4805481279340267e+00,  -6.7675613963809832e-04,
+       2.0241911445804391e-02,   3.8608298760715378e+00,   6.3558641899842260e-04,
+       2.3517745856009110e-02,  -3.3125736597743227e+00,  -4.8591507683128695e-04,
+       2.7323722447292573e-02,   2.8648088091590589e+00,   5.1892328126100203e-04,
+       3.1745636378067953e-02,  -2.4710577422247479e+00,  -3.3190335155472070e-04,
+       3.6883167401240015e-02,   2.1450315408533416e+00,   4.6189809360776176e-04,
+       4.2852126867040180e-02,  -1.8334353019592327e+00,  -1.8326476919948130e-04,
+       4.9787068367863944e-02,   1.5850020809005190e+00,   4.7669939315323097e-04,
+       5.7844320874838456e-02,  -1.3468969891769780e+00,  -1.7380345519175726e-05,
+       6.7205512739749784e-02,   1.1802299801807625e+00,   5.9009214750893949e-04,
+       7.8081666001153169e-02,  -9.9988174688478793e-01,   2.1645139320505843e-04,
+       9.0717953289412512e-02,   8.8503813256539254e-01,   8.5203135609860704e-04,
+       1.0539922456186433e-01,  -7.3165077099639619e-01,   5.9560990889710838e-04,
+       1.2245642825298191e-01,   6.5909386165012596e-01,   1.3651107378683781e-03,
+       1.4227407158651359e-01,  -5.3038429622108840e-01,   1.2606987195022564e-03,
+       1.6529888822158656e-01,   5.0119791866928076e-01,   2.3131990435032663e-03,
+       1.9204990862075413e-01,  -3.8269840749371159e-01,   2.4572002938857678e-03,
+       2.2313016014842982e-01,   3.8622329595139565e-01,   4.0408430887840449e-03,
+       2.5924026064589156e-01,  -2.6413330193320073e-01,   4.6278078809669602e-03,
+       3.0119421191220208e-01,   3.0353632730294311e-01,   7.1437051276295131e-03,
+       3.4993774911115533e-01,  -1.7255655176111537e-01,   8.5723466849983495e-03,
+       4.0656965974059917e-01,   2.5119774955173280e-01,   1.2684763573137947e-02,
+       4.7236655274101469e-01,  -9.8536724013140092e-02,   1.5643387012124067e-02,
+       5.4881163609402650e-01,   2.1755876398162183e-01,   2.2480928663078600e-02,
+       6.3762815162177333e-01,  -3.4268716744688760e-02,   2.8124131719595692e-02,
+       7.4081822068171788e-01,   1.9925218957836366e-01,   3.9373999883133115e-02,
+       8.6070797642505781e-01,   1.8319735495994052e-02,   4.9445586323210833e-02,
+       1.0000000000000000e+00,   1.8963099219918259e-01,   6.7326587032714463e-02,
+       1.1618342427282831e+00,   5.7228135568732394e-02,   8.3541701874077570e-02,
+       1.3498588075760032e+00,   1.7266316834158107e-01,   1.0961776964853986e-01,
+       1.5683121854901687e+00,   6.8141322181604499e-02,   1.3118216481048459e-01,
+       1.8221188003905089e+00,   1.2468074033081850e-01,   1.6144181878027153e-01,
+       2.1170000166126748e+00,   2.1678852838804014e-02,   1.7704476632134886e-01,
+       2.4596031111569494e+00,   1.1114005126278175e-02,   1.9032654055463888e-01,
+       2.8576511180631639e+00,  -1.0424806190544497e-01,   1.6333927603825021e-01,
+       3.3201169227365472e+00,  -1.6473681128667569e-01,   1.1034442879456068e-01,
+       3.8574255306969740e+00,  -2.3603153458714107e-01,  -1.1282682226217962e-02,
+       4.4816890703380645e+00,  -2.2093965064386309e-01,  -1.4579378661401318e-01,
+       5.2069798271798486e+00,  -7.5633542915308175e-02,  -2.7560051939484942e-01,
+       6.0496474644129448e+00,   1.3358180223826097e-01,  -2.3333751023296440e-01,
+       7.0286875805892928e+00,   3.3949946683489907e-01,  -5.9615109981928909e-03,
+       8.1661699125676499e+00,   1.2815187347111337e-01,   3.2380356528743487e-01,
+       9.4877358363585262e+00,  -2.2988301163130145e-01,   2.1970582679149839e-01,
+       1.1023176380641601e+01,  -3.3425750283830036e-01,  -2.8302631898505476e-01,
+       1.2807103782663029e+01,   4.4350537603751145e-01,  -2.2706962776315812e-01,
+       1.4879731724872830e+01,  -8.8943820418669634e-02,   4.7351258711649669e-01,
+       1.7287781840567639e+01,  -1.8646079800862164e-01,  -3.5417866045339608e-01,
+       2.0085536923187668e+01,   2.4494657419883456e-01,   1.6582378621661517e-01,
+       2.3336064580942711e+01,  -2.0169045144304532e-01,  -5.1221107687420810e-02,
+       2.7112638920657883e+01,   1.4661206655803793e-01,   3.5484710794282063e-03,
+       3.1500392308747923e+01,  -1.0564640256629308e-01,   1.1614894738175324e-02,
+       3.6598234443677974e+01,   7.8487036158411266e-02,  -1.4776256489774963e-02,
+       4.2521082000062783e+01,  -6.0533748554794195e-02,   1.4194293010344678e-02,
+       4.9402449105530167e+01,   4.8243702864613026e-02,  -1.2609914713728791e-02,
+       5.7397457045446188e+01,  -3.9347085461672239e-02,   1.0854082569077052e-02,
+       6.6686331040925154e+01,   3.2489421068688185e-02,  -9.2082270347668624e-03,
+       7.7478462925260828e+01,  -2.6982535264609676e-02,   7.7880648968821110e-03,
+       9.0017131300521811e+01,   2.2530196869950080e-02,  -6.6089268276601255e-03,
+       1.0458498557711414e+02,  -1.8947601435977172e-02,   5.6159700146012417e-03,
+       1.2151041751873485e+02,   1.6017457455233256e-02,  -4.7432063636330263e-03,
+       1.4117496392147686e+02,  -1.3519422964231352e-02,   3.9609893136500528e-03,
+       1.6402190729990167e+02,   1.1318328695851308e-02,  -3.2753768787828126e-03,
+       1.9056626845862999e+02,  -9.3839154851987506e-03,   2.6945716306237466e-03,
+       2.2140641620418697e+02,   7.7256174599644543e-03,  -2.2042319512562145e-03,
+       2.5723755590577474e+02,  -6.3199190181430056e-03,   1.7733135127602079e-03,
+       2.9886740096706029e+02,   5.0986473606509210e-03,  -1.3773733375919272e-03,
+       3.4723438047873447e+02,  -3.9929354358609528e-03,   1.0137885881408651e-03,
+       4.0342879349273511e+02,   2.9783618569305080e-03,  -6.9751488719640639e-04,
+       4.6871738678241655e+02,  -2.0802747552777045e-03,   4.4545125438205673e-04,
+       5.4457191012592898e+02,   1.3429398653973710e-03,  -2.6373575275283686e-04,
+       6.3270229281225352e+02,  -7.9345560431147465e-04,   1.4519595835116970e-04,
+       7.3509518924197266e+02,   4.2530878973518046e-04,  -7.4640168948626184e-05,
+       8.5405876252615155e+02,  -2.0457624610548748e-04,   3.5826939350044606e-05,
+       9.9227471560502534e+02,   8.6750842046621606e-05,  -1.5854604622793124e-05,
+       1.1528587427833875e+03,  -3.1406113278782205e-05,   6.2412989356183992e-06,
+       1.3394307643944169e+03,   9.1385289919391839e-06,  -2.0349222128793154e-06,
+       1.5561965278371533e+03,  -1.8949818224609619e-06,   4.8072849734177625e-07,
+       1.8080424144560632e+03,   2.0794387557779629e-07,  -6.0462736574031818e-08).finished();
+
+    // ====================  LIFECYCLE     =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey101
+    //      Method:  FHTKey101
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    FHTKey101::FHTKey101 (const std::string& name) : HankelTransform(name) {
+
+    }  // -----  end of method FHTKey101::FHTKey101  (constructor)  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey101
+    //      Method:  New()
+    // Description:  public constructor
+    //--------------------------------------------------------------------------------------
+    FHTKey101* FHTKey101::New() {
+        FHTKey101*  Obj = new FHTKey101("FHTKey101");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey101
+    //      Method:  ~FHTKey101
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    FHTKey101::~FHTKey101 () {
+
+    }  // -----  end of method FHTKey101::~FHTKey101  (destructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey101
+    //      Method:  Delete
+    // Description:  public destructor
+    //--------------------------------------------------------------------------------------
+    void FHTKey101::Delete() {
+        this->DetachFrom(this);
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey101
+    //      Method:  Release
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    void FHTKey101::Release() {
+        delete this;
+    }
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey101
+    //      Method:  Zgauss
+    //--------------------------------------------------------------------------------------
+    Complex FHTKey101::Zgauss ( const int &ikk, const EMMODE &imode,
+                            const int &itype, const Real &rho,
+                            const Real &wavef, KernelEm1DBase *Kernel ) {
+ 		return Zans(0, Kernel->GetManagerIndex());
+    }		// -----  end of method FHTKey101::ComputeRelated  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey101
+    //      Method:  ComputeRelated
+    //--------------------------------------------------------------------------------------
+    void FHTKey101::ComputeRelated ( const Real& rho, KernelEm1DBase* Kernel ) {
+        return ;
+    }		// -----  end of method FHTKey101::ComputeRelated  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey101
+    //      Method:  ComputeRelated
+    //--------------------------------------------------------------------------------------
+    void FHTKey101::ComputeRelated ( const Real& rho, std::vector< KernelEm1DBase* > KernelVec ) {
+        return ;
+    }		// -----  end of method FHTKey101::ComputeRelated  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey101
+    //      Method:  ComputeRelated
+    //--------------------------------------------------------------------------------------
+    void FHTKey101::ComputeRelated ( const Real& rho, KernelEM1DManager* KernelManager ) {
+
+        //kernelVec = KernelManager->GetSTLVector();
+        int nrel = (int)(KernelManager->GetSTLVector().size());
+        Eigen::Matrix<Complex, 101, Eigen::Dynamic > Zwork;
+        // TODO, if we want to allow lagged, then 1 below should be nlag
+        Zans= Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic>::Zero(1, nrel);
+        Zwork.resize(101, nrel);
+        VectorXr lambda = WT101.col(0).array()/rho;
+        int NumFun = 0;
+        int idx = 0;
+
+        // Get Kernel values
+        for (int ir=0; ir<lambda.size(); ++ir) {
+            // irelated loop
+            ++NumFun;
+            KernelManager->ComputeReflectionCoeffs(lambda(ir), idx, rho);
+            for (int ir2=0; ir2<nrel; ++ir2) {
+                // Zwork* needed due to sign convention of filter weights
+ 			    Zwork(ir, ir2) = std::conj(KernelManager->GetSTLVector()[ir2]->RelBesselArg(lambda(ir)));
+            }
+
+        }
+
+        // We diverge slightly from Key here, each kernel is evaluated seperately, whereby instead
+        // they prefer to sum them. The reason is that all those terms have been removed from the kernels
+        // in the interests of making them as generic and reusable as possible. This approach requires slightly
+        // more multiplies, but the same number of kernel evaluations, which is the expensive part.
+        // Inner product and scale
+        for (int ir2=0; ir2<nrel; ++ir2) {
+            Zans(0, ir2) = Zwork.col(ir2).dot(WT101.col(KernelManager->GetSTLVector()[ir2]->GetBesselOrder() + 1))/rho;
+        }
+
+        return ;
+    }		// -----  end of method FHTKey101::ComputeRelated  -----
+
+}		// -----  end of Lemma  name  -----

Modules/FDEM1D/src/FHTKey51.cpp

@@ -0,0 +1,209 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      02/11/2014 03:42:53 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#include "FHTKey51.h"
+
+namespace Lemma {
+
+    // ====================  FRIEND METHODS  =====================
+
+    std::ostream &operator<<(std::ostream &stream, const FHTKey51 &ob) {
+
+        stream << *(HankelTransform*)(&ob);
+
+        return stream;
+    }
+
+
+    // ====================  STATIC CONST MEMBERS     ============
+
+    const Eigen::Matrix<Real, 51, 3>  FHTKey51::WT51 =
+        ( Eigen::Matrix<Real, 51, 3>()   <<
+        // Base                   J0                      J1
+           4.9915939069102170e-03,   6.5314496156480717e-02,   3.8409924166118657e-05,
+           6.1703482511978082e-03,  -2.2265895125268051e-01,  -9.4382633059055269e-05,
+           7.6274629409160176e-03,   4.2794928430042073e-01,   1.6377612356675232e-04,
+           9.4286721829279947e-03,  -5.8890658905204007e-01,  -1.7853487610334151e-04,
+           1.1655233178024955e-02,   6.7897324897038758e-01,   1.9759569268356316e-04,
+           1.4407591843112350e-02,  -6.8296549495756353e-01,  -1.2796247718553291e-04,
+           1.7809914185937643e-02,   6.4702210424566342e-01,   1.3163370416771999e-04,
+           2.2015687754376449e-02,  -5.6843090153083187e-01,   1.7066927559149181e-05,
+           2.7214645856121149e-02,   4.9960500362966542e-01,   4.1368007808198310e-05,
+           3.3641326918204623e-02,  -4.0923517268678855e-01,   2.3582259002758631e-04,
+           4.1585655121173182e-02,   3.5487831784012780e-01,  -1.9929745662753875e-05,
+           5.1406019627642255e-02,  -2.7408257835871558e-01,   5.8196110748926486e-04,
+           6.3545442443014022e-02,   2.4668368971888163e-01,   1.1164151202379049e-05,
+           7.8551564282309541e-02,  -1.7348161774657314e-01,   1.2053942009238238e-03,
+           9.7101350057185065e-02,   1.7509173908347012e-01,   2.8328713800714110e-04,
+           1.2003162851145673e-01,  -1.0007796678766585e-01,   2.4375075610646724e-03,
+           1.4837684372696586e-01,   1.3297302593795621e-01,   1.1709289200267103e-03,
+           1.8341572156771246e-01,  -4.3822390117083297e-02,   5.0080095645252103e-03,
+           2.2672895630607542e-01,   1.1415804492335258e-01,   3.5856849047131551e-03,
+           2.8027051982381157e-01,   4.2584271963990363e-03,   1.0536604059335859e-02,
+           3.4645581033005746e-01,   1.1496183925974515e-01,   9.6674718436839564e-03,
+           4.2827061721265969e-01,   5.1313336759457658e-02,   2.2583365267100426e-02,
+           5.2940581770869455e-01,   1.3312389010285514e-01,   2.4201911801947001e-02,
+           6.5442388190885858e-01,   1.0111673764393908e-01,   4.8602551164692191e-02,
+           8.0896469756649991e-01,   1.6331446488042209e-01,   5.6856974938076565e-02,
+           1.0000000000000000e+00,   1.4704406144951229e-01,   1.0202078096072606e-01,
+           1.2361478850785035e+00,   1.8341391219815678e-01,   1.2202639829343022e-01,
+           1.5280615937840571e+00,   1.5073655145087875e-01,   1.9561985197118459e-01,
+           1.8889101074258496e+00,   1.2356364992866918e-01,   2.1570853920674185e-01,
+           2.3349722343978727e+00,   1.1529465836107913e-02,   2.8552388758852060e-01,
+           2.8863709892679585e+00,  -1.2852626053530605e-01,   2.0559964796530625e-01,
+           3.5679813939355345e+00,  -2.9874216118407571e-01,   1.1666011451374350e-01,
+           4.4105526541128617e+00,  -3.1330553036684633e-01,  -2.3636714743601936e-01,
+           5.4520953354089947e+00,  -3.2332453606385231e-02,  -3.4036030266164258e-01,
+           6.7395961181122024e+00,   4.2056051544727674e-01,  -1.9475364255836261e-01,
+           8.3311374876876929e+00,   1.3883637369942961e-01,   5.7608115965662166e-01,
+           1.0298517985703377e+01,  -5.0223684329542873e-01,  -2.1471464584834585e-01,
+           1.2730491227470161e+01,   3.7996073748731690e-01,  -1.2611070492338947e-01,
+           1.5736769806847677e+01,  -1.7984404170109178e-01,   2.0019703515125831e-01,
+           1.9452974714702009e+01,   7.0557286965350657e-02,  -1.6147664664730754e-01,
+           2.4046753552064487e+01,  -2.7522277139686569e-02,   1.1398023016900673e-01,
+           2.9725343546388515e+01,   1.1909130661901874e-02,  -7.9924455203352035e-02,
+           3.6744920558100112e+01,  -5.8977428045126450e-03,   5.7024556382799692e-02,
+           4.5422155835273074e+01,   3.2648420034561555e-03,  -4.1006636508593382e-02,
+           5.6148501871478999e+01,  -1.9304039780209286e-03,   2.9192063091319696e-02,
+           6.9407851838755207e+01,   1.1594138315987755e-03,  -2.0089573135329029e-02,
+           8.5798369258319340e+01,  -6.7050941490060716e-04,   1.2965400526524978e-02,
+           1.0605947270185592e+02,   3.5089803807606258e-04,  -7.5154910983038946e-03,
+           1.3110519287294045e+02,  -1.5287051174029577e-04,   3.6269079130258285e-03,
+           1.6206540689269471e+02,   4.8238483411813232e-05,  -1.2668720233377250e-03,
+           2.0033680997479166e+02,  -8.0433917146487977e-06,   2.3403502580547994e-04).finished();
+
+    // ====================  LIFECYCLE     =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey51
+    //      Method:  FHTKey51
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    FHTKey51::FHTKey51 (const std::string& name) : HankelTransform(name) {
+
+    }  // -----  end of method FHTKey51::FHTKey51  (constructor)  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey51
+    //      Method:  New()
+    // Description:  public constructor
+    //--------------------------------------------------------------------------------------
+    FHTKey51* FHTKey51::New() {
+        FHTKey51*  Obj = new FHTKey51("FHTKey51");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey51
+    //      Method:  ~FHTKey51
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    FHTKey51::~FHTKey51 () {
+
+    }  // -----  end of method FHTKey51::~FHTKey51  (destructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey51
+    //      Method:  Delete
+    // Description:  public destructor
+    //--------------------------------------------------------------------------------------
+    void FHTKey51::Delete() {
+        this->DetachFrom(this);
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey51
+    //      Method:  Release
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    void FHTKey51::Release() {
+        delete this;
+    }
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey51
+    //      Method:  Zgauss
+    //--------------------------------------------------------------------------------------
+    Complex FHTKey51::Zgauss ( const int &ikk, const EMMODE &imode,
+                            const int &itype, const Real &rho,
+                            const Real &wavef, KernelEm1DBase *Kernel ) {
+ 		return Zans(0, Kernel->GetManagerIndex());
+    }		// -----  end of method FHTKey51::ComputeRelated  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey51
+    //      Method:  ComputeRelated
+    //--------------------------------------------------------------------------------------
+    void FHTKey51::ComputeRelated ( const Real& rho, KernelEm1DBase* Kernel ) {
+        return ;
+    }		// -----  end of method FHTKey51::ComputeRelated  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey51
+    //      Method:  ComputeRelated
+    //--------------------------------------------------------------------------------------
+    void FHTKey51::ComputeRelated ( const Real& rho, std::vector< KernelEm1DBase* > KernelVec ) {
+        return ;
+    }		// -----  end of method FHTKey51::ComputeRelated  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  FHTKey51
+    //      Method:  ComputeRelated
+    //--------------------------------------------------------------------------------------
+    void FHTKey51::ComputeRelated ( const Real& rho, KernelEM1DManager* KernelManager ) {
+
+        //kernelVec = KernelManager->GetSTLVector();
+        int nrel = (int)(KernelManager->GetSTLVector().size());
+        Eigen::Matrix<Complex, 51, Eigen::Dynamic > Zwork;
+        // TODO, if we want to allow lagged, then 1 below should be nlag
+        Zans= Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic>::Zero(1, nrel);
+        Zwork.resize(51, nrel);
+        VectorXr lambda = WT51.col(0).array()/rho;
+        int NumFun = 0;
+        int idx = 0;
+
+        // Get Kernel values
+        for (int ir=0; ir<lambda.size(); ++ir) {
+            // irelated loop
+            ++NumFun;
+            KernelManager->ComputeReflectionCoeffs(lambda(ir), idx, rho);
+            for (int ir2=0; ir2<nrel; ++ir2) {
+                // Zwork* needed due to sign convention of filter weights
+ 			    Zwork(ir, ir2) = std::conj(KernelManager->GetSTLVector()[ir2]->RelBesselArg(lambda(ir)));
+            }
+
+        }
+
+        // We diverge slightly from Key here, each kernel is evaluated seperately, whereby instead
+        // they prefer to sum them. The reason is that all those terms have been removed from the kernels
+        // in the interests of making them as generic and reusable as possible. This approach requires slightly
+        // more multiplies, but the same number of kernel evaluations, which is the expensive part.
+        // Inner product and scale
+        for (int ir2=0; ir2<nrel; ++ir2) {
+            Zans(0, ir2) = Zwork.col(ir2).dot(WT51.col(KernelManager->GetSTLVector()[ir2]->GetBesselOrder() + 1))/rho;
+        }
+
+        return ;
+    }		// -----  end of method FHTKey51::ComputeRelated  -----
+
+}		// -----  end of Lemma  name  -----

Modules/FDEM1D/src/GroundedElectricDipole.cpp

@@ -0,0 +1,85 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      01/29/2014 07:05:13 AM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#include "GroundedElectricDipole.h"
+
+
+namespace Lemma {
+
+    // ====================  FRIEND METHODS  =====================
+
+    std::ostream &operator<<(std::ostream &stream, const GroundedElectricDipole &ob) {
+
+        stream << *(DipoleSource*)(&ob);
+
+        return stream;
+    }
+
+    // ====================  LIFECYCLE     =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  GroundedElectricDipole
+    //      Method:  GroundedElectricDipole
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    GroundedElectricDipole::GroundedElectricDipole (const std::string& name) : DipoleSource(name) {
+
+    }  // -----  end of method GroundedElectricDipole::GroundedElectricDipole  (constructor)  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  GroundedElectricDipole
+    //      Method:  New()
+    // Description:  public constructor
+    //--------------------------------------------------------------------------------------
+    GroundedElectricDipole* GroundedElectricDipole::New() {
+        GroundedElectricDipole*  Obj = new GroundedElectricDipole("GroundedElectricDipole");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  GroundedElectricDipole
+    //      Method:  ~GroundedElectricDipole
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    GroundedElectricDipole::~GroundedElectricDipole () {
+
+    }  // -----  end of method GroundedElectricDipole::~GroundedElectricDipole  (destructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  GroundedElectricDipole
+    //      Method:  Delete
+    // Description:  public destructor
+    //--------------------------------------------------------------------------------------
+    void GroundedElectricDipole::Delete() {
+        this->DetachFrom(this);
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  GroundedElectricDipole
+    //      Method:  Release
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    void GroundedElectricDipole::Release() {
+        delete this;
+    }
+
+}		// -----  end of Lemma  name  -----
+

Modules/FDEM1D/src/LayeredEarthEMReader.cpp

@@ -0,0 +1,124 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      09/27/2013 01:44:46 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2013, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2013, Trevor Irons
+ */
+
+#include "LayeredEarthEMReader.h"
+
+namespace Lemma {
+
+    // ====================  FRIEND METHODS  =====================
+
+    std::ostream &operator<<(std::ostream &stream, const LayeredEarthEMReader &ob) {
+
+        stream << *(LemmaObject*)(&ob);
+
+        return stream;
+    }
+
+    // ====================  LIFECYCLE     =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  LayeredEarthEMReader
+    //      Method:  LayeredEarthEMReader
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    LayeredEarthEMReader::LayeredEarthEMReader (const std::string& name) : LemmaObject(name),
+        LayEarth(NULL) {
+
+    }  // -----  end of method LayeredEarthEMReader::LayeredEarthEMReader  (constructor)  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  LayeredEarthEMReader
+    //      Method:  New()
+    // Description:  public constructor
+    //--------------------------------------------------------------------------------------
+    LayeredEarthEMReader* LayeredEarthEMReader::New() {
+        LayeredEarthEMReader*  Obj = new LayeredEarthEMReader("LayeredEarthEMReader");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  LayeredEarthEMReader
+    //      Method:  ~LayeredEarthEMReader
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    LayeredEarthEMReader::~LayeredEarthEMReader () {
+        if (LayEarth) LayEarth->Delete();
+    }  // -----  end of method LayeredEarthEMReader::~LayeredEarthEMReader  (destructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  LayeredEarthEMReader
+    //      Method:  Delete
+    // Description:  public destructor
+    //--------------------------------------------------------------------------------------
+    void LayeredEarthEMReader::Delete() {
+        this->DetachFrom(this);
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  LayeredEarthEMReader
+    //      Method:  Release
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    void LayeredEarthEMReader::Release() {
+        delete this;
+    }
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  LayeredEarthEMReader
+    //      Method:  GetLayeredEarth
+    //--------------------------------------------------------------------------------------
+    LayeredEarthEM* LayeredEarthEMReader::GetLayeredEarth (  ) {
+        return LayEarth;
+    }		// -----  end of method LayeredEarthEMReader::GetLayeredEarth  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  LayeredEarthEMReader
+    //      Method:  ReadASCIIInputFile
+    //--------------------------------------------------------------------------------------
+    void LayeredEarthEMReader::ReadASCIIInputFile ( const std::string& name ) {
+        if (LayEarth) LayEarth->Delete();
+        ASCIIParser* Parser = ASCIIParser::New();
+        LayEarth = LayeredEarthEM::New();
+
+        Parser->SetCommentString("//");
+        Parser->Open(name);
+
+        int nlay = Parser->ReadInts( 1 )[0]; // non-air layers
+            LayEarth->SetNumberOfLayers(nlay+1);
+
+        VectorXcr sigma = VectorXcr::Zero(nlay+1);
+        VectorXr  thick(nlay-1);
+        for (int ilay=1; ilay<nlay; ++ilay) {
+            std::vector<Real> rval = Parser->ReadReals(2);
+            sigma(ilay) =  1./rval[0];
+            thick(ilay-1) =  rval[1]; //CondMod[ilay+1];
+        }
+        sigma(nlay) = 1./Parser->ReadReals(1)[0];
+        LayEarth->SetLayerConductivity(sigma);
+        if (thick.size() > 0) LayEarth->SetLayerThickness(thick);
+        Parser->Delete();
+        return ;
+    }		// -----  end of method LayeredEarthEMReader::ReadASCIIInputFile  -----
+
+
+}		// -----  end of Lemma  name  -----

Modules/FDEM1D/src/MagneticDipole.cpp

@@ -0,0 +1,82 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      09/25/2013 08:20:14 AM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2013, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2013, Trevor Irons
+ */
+
+#include "MagneticDipole.h"
+
+namespace Lemma {
+
+    // ====================  FRIEND METHODS  =====================
+
+    std::ostream &operator<<(std::ostream &stream, const MagneticDipole &ob) {
+
+        stream << *(DipoleSource*)(&ob);
+
+        return stream;
+    }
+    // ====================  LIFECYCLE     =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  MagneticDipole
+    //      Method:  MagneticDipole
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    MagneticDipole::MagneticDipole (const std::string& name) : DipoleSource(name) {
+
+    }  // -----  end of method MagneticDipole::MagneticDipole  (constructor)  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  MagneticDipole
+    //      Method:  New()
+    // Description:  public constructor
+    //--------------------------------------------------------------------------------------
+    MagneticDipole* MagneticDipole::New() {
+        MagneticDipole*  Obj = new MagneticDipole("MagneticDipole");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  MagneticDipole
+    //      Method:  ~MagneticDipole
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    MagneticDipole::~MagneticDipole () {
+
+    }  // -----  end of method MagneticDipole::~MagneticDipole  (destructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  MagneticDipole
+    //      Method:  Delete
+    // Description:  public destructor
+    //--------------------------------------------------------------------------------------
+    void MagneticDipole::Delete() {
+        this->DetachFrom(this);
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  MagneticDipole
+    //      Method:  Release
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    void MagneticDipole::Release() {
+        delete this;
+    }
+
+} // namespace Lemma

Modules/FDEM1D/src/PolygonalWireAntenna.cpp

@@ -0,0 +1,349 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     05/18/2010
+  @version  $Id: PolygonalWireAntenna.cpp 211 2015-02-27 05:43:26Z tirons $
+ **/
+
+#include "PolygonalWireAntenna.h"
+
+namespace Lemma {
+
+#ifdef HAVE_YAMLCPP
+    std::ostream &operator << (std::ostream &stream, const PolygonalWireAntenna &ob) {
+        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
+        return stream;
+    }
+#else
+	std::ostream &operator<<(std::ostream &stream,
+				const PolygonalWireAntenna &ob) {
+
+		stream << *(WireAntenna*)(&ob);
+		//stream << "Current: " << ob.Current << " [A]\n";
+		//stream << "Frequencies: " << ob.Freqs.transpose() << " [Hz]\n";
+		//stream << "Number of points " << ob.NumberOfPoints << "\n";
+		//stream << "Points:\n" << ob.Points.transpose() << "\n";
+		//stream << "Dipoles used to approximate " << ob.Dipoles.size();
+		return stream;
+	}
+#endif
+	// ====================  LIFECYCLE     =======================
+
+	PolygonalWireAntenna::PolygonalWireAntenna(const std::string& name)
+		: WireAntenna(name), minDipoleRatio(.15),
+   		minDipoleMoment(1e-6), maxDipoleMoment(1e1), rRepeat(1e10,1e10,1e10) {
+		Points.setZero();
+        //rRepeat.setOnes();
+	}
+
+#ifdef HAVE_YAMLCPP
+    PolygonalWireAntenna::PolygonalWireAntenna(const YAML::Node& node)
+		: WireAntenna(node) {
+// minDipoleRatio(.15),
+// minDipoleMoment(1e-4),
+// maxDipoleMoment(1e-0)
+        minDipoleRatio   = node["minDipoleRatio"].as<Real>();
+        maxDipoleMoment  = node["maxDipoleMoment"].as<Real>();
+        minDipoleMoment  = node["minDipoleMoment"].as<Real>();
+	}
+#endif
+
+	PolygonalWireAntenna::~PolygonalWireAntenna() {
+        if (this->NumberOfReferences != 0)
+            throw DeleteObjectWithReferences( this );
+		// Taken care of in parent
+        //for (unsigned int id=0; id<Dipoles.size(); ++id) {
+		//	Dipoles[id]->Delete();
+		//}
+		//Dipoles.clear();
+	}
+
+	PolygonalWireAntenna* PolygonalWireAntenna::New() {
+		PolygonalWireAntenna* Obj = new
+            PolygonalWireAntenna("PolygonalWireAntenna");
+        Obj->AttachTo(Obj);
+        return Obj;
+	}
+
+	PolygonalWireAntenna* PolygonalWireAntenna::Clone() {
+		PolygonalWireAntenna* copy = PolygonalWireAntenna::New();
+		//copy->AttachTo(copy); // NO! Attached above!
+        copy->minDipoleRatio = this->minDipoleRatio;
+		copy->minDipoleMoment = this->minDipoleMoment;
+		copy->maxDipoleMoment = this->maxDipoleMoment;
+		copy->NumberOfPoints = this->NumberOfPoints;
+		copy->Freqs = this->Freqs;
+		copy->Current = this->Current;
+		copy->NumberOfTurns = this->NumberOfTurns;
+		copy->Points = this->Points;
+		//copy->Dipoles = this->Dipoles; // no, disaster
+		return copy;
+	}
+
+	void PolygonalWireAntenna::Delete() {
+		this->DetachFrom(this);
+	}
+
+    void PolygonalWireAntenna::Release() {
+		delete this;
+	}
+
+    void PolygonalWireAntenna::SetMinDipoleRatio (const Real& ratio) {
+        minDipoleRatio = ratio;
+    }
+
+    void PolygonalWireAntenna::SetMinDipoleMoment (const Real& m) {
+        minDipoleMoment = m;
+    }
+
+    void PolygonalWireAntenna::SetMaxDipoleMoment (const Real& m) {
+        maxDipoleMoment = m;
+    }
+
+	// ====================  OPERATIONS    =======================
+
+	void PolygonalWireAntenna::ApproximateWithElectricDipoles(const Vector3r &rp) {
+        // Only resplit if necessary. Save a few cycles if repeated
+        if ( (rRepeat-rp).norm() > 1e-16 ) {
+		    for (unsigned int id=0; id<Dipoles.size(); ++id) {
+			    Dipoles[id]->Delete();
+		    }
+		    Dipoles.clear();
+
+		    // loop over all segments
+		    for (int iseg=0; iseg<NumberOfPoints-1; ++iseg) {
+			    InterpolateLineSegment(Points.col(iseg), Points.col(iseg+1), rp);
+		    }
+            rRepeat = rp;
+
+        } else {
+            for (unsigned int id=0; id<Dipoles.size(); ++id) {
+                Dipoles[id]->SetFrequencies(Freqs);
+            }
+        }
+	}
+
+	Vector3r PolygonalWireAntenna::ClosestPointOnLine(const Vector3r &p1,
+					const Vector3r &p2, const Vector3r &tp) {
+
+		Vector3r v1 = p2 - p1;
+		Vector3r v2 = p1 - tp;
+		Vector3r v3 = p1 - p2;
+		Vector3r v4 = p2 - tp;
+
+		Real dot1 = v2.dot(v1);
+		Real dot2 = v1.dot(v1);
+		Real dot3 = v4.dot(v3);
+		Real dot4 = v3.dot(v3);
+		Real t1 = -1.*dot1/dot2;
+		Real t2 = -1.*dot3/dot4;
+
+		Vector3r pos =  p1+v1*t1 ;
+
+		// check if on line
+		//	else give back the closest end point
+		if ( t1>=0 && t2>=0. ) {
+			return pos;
+		} else if (t1<0) {
+			return p1;
+		} else {
+			return p2;
+		}
+	}
+
+	void PolygonalWireAntenna::PushXYZDipoles(const Vector3r &step,
+				    const Vector3r &cp, const Vector3r &dir,
+					std::vector<DipoleSource*> &xDipoles) {
+
+		Real scale = (Real)(NumberOfTurns)*Current;
+
+        DipoleSource *tx = DipoleSource::New();
+		    tx->SetLocation(cp);
+		    tx->SetType(UNGROUNDEDELECTRICDIPOLE);
+			tx->SetPolarisation(dir);
+			tx->SetFrequencies(Freqs);
+			tx->SetMoment(scale*step.norm());
+			xDipoles.push_back(tx);
+	}
+
+	void PolygonalWireAntenna::CorrectOverstepXYZDipoles(const Vector3r &step,
+				    const Vector3r &cp,	const Vector3r &dir,
+					std::vector<DipoleSource*> &xDipoles ) {
+
+		Real scale = (Real)(NumberOfTurns)*Current;
+
+		// X oriented dipoles
+		if (step.norm() > minDipoleMoment) {
+			xDipoles[xDipoles.size()-1]->SetLocation(cp);
+			xDipoles[xDipoles.size()-1]->SetMoment(scale*step.norm());
+		}
+	}
+
+	void PolygonalWireAntenna::InterpolateLineSegment(const Vector3r &p1,
+					const Vector3r &p2, const Vector3r & tp) {
+
+
+		Vector3r phat = (p1-p2).array() / (p1-p2).norm();
+		Vector3r c    = this->ClosestPointOnLine(p1, p2, tp);
+		Real dtp = (tp-c).norm();    // distance to point at c
+		Real dc1 = (p1-c).norm();    // distance to c from p1
+		Real dc2 = (p2-c).norm();    // distance to c from p1
+
+        // unit vector
+		Vector3r cdir = (p2-p1).array() / (p2-p1).norm();
+
+		///////////////////
+		// dipoles for this segment
+		std::vector<DipoleSource*>           xDipoles;
+
+		// go towards p1
+		if ( ((c-p1).array().abs() > minDipoleMoment).any() ) {
+
+			// cp = current pos, lp = last pos
+			Vector3r cp = c + phat*(dtp*minDipoleRatio)*.5;
+			Vector3r lp = c;
+ 			Real dist = (cp-p1).norm();
+ 			Real dist_old = dist+1.;
+
+			// check that we didn't run past the end, or that we aren't starting at
+			// the end, or that initial step runs over!
+			Vector3r dir = (p1-cp).array() / (p1-cp).norm();   // direction of movement
+			Vector3r step = phat*(dtp*minDipoleRatio);
+ 			Vector3r stepold = Vector3r::Zero();
+
+			// (dir-phat) just shows if we are stepping towards or away  from p1
+			while (dist < dist_old && (dir-phat).norm() < 1e-8) {
+
+				PushXYZDipoles(step, cp, cdir, xDipoles);
+
+				// Make 1/2 of previous step, 1/2 of this step, store this step
+				stepold  = step;
+				step     = phat*( (cp-tp).norm()*minDipoleRatio );
+			    while ( (step.array().abs() > maxDipoleMoment).any() ) {
+				    step *= .5;
+			    }
+				lp       = cp;
+				cp      += .5*stepold + .5*step;
+				dist     = (cp-p1).norm();
+				dir      = (p1-cp).array() / (p1-cp).norm();
+			}
+
+			// cp now points to end last of dipole moments
+			cp -= .5*step;
+
+			// Fix last dipole position, so that entire wire is represented,
+			// and no more
+			Real distLastSeg = (c - cp).norm();
+
+			if (distLastSeg + minDipoleMoment < dc1) {
+				// case 1: understep, add dipole
+				step  = (p1-cp).array();
+				cp   += .5*step;
+				PushXYZDipoles(step, cp, cdir, xDipoles);
+			} else if (distLastSeg > dc1 + minDipoleMoment) {
+				// case 2: overstep, reposition dipole and size
+				step  = (p1 - (lp-.5*stepold));
+				cp =  (lp-.5*stepold) + (.5*step);
+				CorrectOverstepXYZDipoles(step, cp, cdir, xDipoles);
+			}
+			// else case 0: nearly 'perfect' fit do nothing
+		}
+
+		// go towards p2
+		if ( ( (c-p2).array().abs() > minDipoleMoment).any() ) {
+
+ 			// cp = current pos, lp = last pos
+ 			Vector3r step = -phat*(dtp*minDipoleRatio);
+			while ( (step.array().abs() > maxDipoleMoment).any() ) {
+				step *= .5;
+			}
+
+ 			Vector3r cp = c + step*.5;
+ 			Vector3r lp = c;
+  			Real dist = (p2-cp).norm();
+  			Real dist_old = dist+1e3;
+
+			// check that we didn't run past the end, or that we aren't starting at
+			// the end, or that initial step runs over!
+			Vector3r dir = (p2-cp).array() / (p2-cp).norm();   // direction of movement
+
+ 			Vector3r stepold = Vector3r::Zero();
+
+ 			// (dir-phat) just shows if we are stepping towards or away  from p1
+ 			while (dist < dist_old && (dir+phat).norm() < 1e-8) {
+
+ 				PushXYZDipoles(step, cp, cdir, xDipoles);
+
+				// Make 1/2 of previous step, 1/2 of this step, store this step
+				stepold  = step;
+				step     = -phat*( (cp-tp).norm()*minDipoleRatio );
+			    while ( (step.array().abs() > maxDipoleMoment).any() ) {
+				    step *= .5;
+			    }
+				lp       = cp;
+				cp      += .5*stepold + .5*step;
+				dist     = (cp-p2).norm();
+				dir      = (p2-cp).array() / (p2-cp).norm();
+			}
+
+			// cp now points to end last of dipole moments
+			cp -= .5*step;
+
+			// Fix last dipole position, so that entire wire is represented,
+			// and no more
+			Real distLastSeg = (c - cp).norm();
+			if (distLastSeg + minDipoleMoment < dc2) {
+				// case 1: understep, add dipole
+				step  = (p2-cp).array();
+				cp   += .5*step;
+				PushXYZDipoles(step, cp, cdir, xDipoles);
+
+			} else if (distLastSeg > dc2 + minDipoleMoment) {
+
+				// case 2: overstep, reposition dipole and size
+				step  = (p2 - (lp-.5*stepold));
+				cp =  (lp-.5*stepold) + (.5*step);
+				CorrectOverstepXYZDipoles(step, cp, cdir, xDipoles);
+
+			}
+			// else case 0: nearly 'perfect' fit do nothing
+		}
+		Dipoles.insert(Dipoles.end(), xDipoles.begin(), xDipoles.end());
+	}
+
+    #ifdef HAVE_YAMLCPP
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  PolygonalWireAntenna
+    //      Method:  Serialize
+    //--------------------------------------------------------------------------------------
+    YAML::Node PolygonalWireAntenna::Serialize (  ) const {
+        YAML::Node node = WireAntenna::Serialize();
+        node.SetTag( this->Name );
+        node["minDipoleRatio"]  = minDipoleRatio;
+        node["maxDipoleMoment"] = maxDipoleMoment;
+        node["minDipoleMoment"] = minDipoleMoment;
+        return node;
+    }		// -----  end of method PolygonalWireAntenna::Serialize  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  WireAntenna
+    //      Method:  DeSerialize
+    //--------------------------------------------------------------------------------------
+    PolygonalWireAntenna* PolygonalWireAntenna::DeSerialize ( const YAML::Node& node ) {
+        PolygonalWireAntenna* Object = new PolygonalWireAntenna(node);
+        Object->AttachTo(Object);
+        DESERIALIZECHECK( node, Object )
+        return Object ;
+    }		// -----  end of method WireAntenna::DeSerialize  -----
+
+    #endif
+
+}

Modules/FDEM1D/src/QWEKey.cpp

@@ -0,0 +1,332 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/*      Original code is port of algorithm published by Key2011
+        %------------------------------------------------------------------%
+        % Copyright (c) 2012 by the Society of Exploration Geophysicists.  %
+        % For more information, go to http://software.seg.org/2012/0003 .  %
+        % You must read and accept usage terms at:                         %
+        % http://software.seg.org/disclaimer.txt before use.               %
+        %------------------------------------------------------------------%
+*/
+
+/**
+ * @file
+ * @date      02/12/2014 10:28:15 AM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#include "QWEKey.h"
+
+//#include <Eigen/Eigenvalues>
+
+namespace Lemma {
+
+    // ====================  FRIEND METHODS  =====================
+
+    std::ostream &operator<<(std::ostream &stream, const QWEKey &ob) {
+
+        stream << *(HankelTransform*)(&ob);
+
+        return stream;
+    }
+
+    // ====================  LIFECYCLE     =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  QWEKey
+    //      Method:  QWEKey
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    //
+    QWEKey::QWEKey (const std::string& name) : HankelTransform(name), RelTol(1e-12), AbsTol(1e-32), nQuad(61), nDelay(1),
+    //QWEKey::QWEKey (const std::string& name) : HankelTransform(name), RelTol(1e-38), AbsTol(1e-48), nQuad(39), nDelay(5),
+        nIntervalsMax(40) {
+        BesselWeights( J0 ); // TODO experiment with zero weight (J0, J1) options, should be static one time method
+    }  // -----  end of method QWEKey::QWEKey  (constructor)  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  QWEKey
+    //      Method:  New()
+    // Description:  public constructor
+    //--------------------------------------------------------------------------------------
+    QWEKey* QWEKey::New() {
+        QWEKey*  Obj = new QWEKey("QWEKey");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  QWEKey
+    //      Method:  ~QWEKey
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    QWEKey::~QWEKey () {
+
+    }  // -----  end of method QWEKey::~QWEKey  (destructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  QWEKey
+    //      Method:  Delete
+    // Description:  public destructor
+    //--------------------------------------------------------------------------------------
+    void QWEKey::Delete() {
+        this->DetachFrom(this);
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  QWEKey
+    //      Method:  Release
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    void QWEKey::Release() {
+        delete this;
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  QWEKey
+    //      Method:  Zgauss
+    //--------------------------------------------------------------------------------------
+    Complex QWEKey::Zgauss ( const int &ikk, const EMMODE &imode,
+                            const int &itype, const Real &rho,
+                            const Real &wavef, KernelEm1DBase *Kernel ) {
+        return Textrap(Kernel->GetManagerIndex(), Tn(Kernel->GetManagerIndex())) ;
+    }		// -----  end of method QWEKey::Zgauss  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  QWEKey
+    //      Method:  ComputeRelated
+    //--------------------------------------------------------------------------------------
+    void QWEKey::ComputeRelated ( const Real& rho, KernelEm1DBase* Kernel ) {
+        return ;
+    }		// -----  end of method QWEKey::ComputeRelated  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  QWEKey
+    //      Method:  ComputeRelated
+    //--------------------------------------------------------------------------------------
+    void QWEKey::ComputeRelated ( const Real& rho, std::vector< KernelEm1DBase* > KernelVec ) {
+        return ;
+    }		// -----  end of method QWEKey::ComputeRelated  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  QWEKey
+    //      Method:  ComputeRelated
+    //--------------------------------------------------------------------------------------
+    void QWEKey::ComputeRelated ( const Real& rho, KernelEM1DManager* KernelManagerIn ) {
+        KernelManager = KernelManagerIn;  // OK becauase this is internal and we know what we are doing
+
+        Lambda = Bx.array()/rho;
+        Intervals = xInt.array()/rho;
+        int nrel = (int)(KernelManager->GetSTLVector().size());
+        Zans = Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic>::Zero(1, nrel);
+        QWE(rho);
+        return ;
+    }		// -----  end of method QWEKey::ComputeRelated  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  QWEKey
+    //      Method:  GaussQuadWeights
+    //--------------------------------------------------------------------------------------
+    void QWEKey::GaussQuadWeights(const int& N) {
+        std::cerr<<"QWEKey needs work to remove Boost, etc." << std::endl;
+        // Below works with older Eigen, need to find problem
+//         VectorXr Nv = VectorXr::LinSpaced(N-1, 1, N-1);
+//         VectorXr beta  = 0.5 / (1.-(2.*Nv.array()).pow(-2)).sqrt();
+//         MatrixXr T = MatrixXr::Zero(N,N);
+//         //std::cerr << "Eigen ERROR BELOW, QWEKey.cpp  QWEKey::GaussQuadWeights, COMMENTED OUT ";
+//         T.bottomLeftCorner(N-1, N-1) = beta.asDiagonal();
+//         Eigen::SelfAdjointEigenSolver<MatrixXr> eig( T.selfadjointView< Eigen::Lower >() ); // PROBLEM LINE
+//             GaussAbscissa = eig.eigenvalues();
+//             GaussWeights = 2.*eig.eigenvectors().row(0).array().pow(2);
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  QWEKey
+    //      Method:  BesselWeights
+    //--------------------------------------------------------------------------------------
+    void QWEKey::BesselWeights ( const sZeroType& sType ) {
+    #ifdef HAVEBOOSTSPECIALFUNCTIONS
+        GaussQuadWeights(nQuad); // TODO should this be moved out of initializer?
+        std::vector<Real> bz;
+        xInt = VectorXr(nIntervalsMax+1);
+        xInt(0) = 1e-20;
+        switch (sType) {
+            case J0:
+                boost::math::cyl_bessel_j_zero(0.0, 1, nIntervalsMax, std::back_inserter(bz));
+                xInt.tail(nIntervalsMax) = VectorXr::Map(&bz[0], nIntervalsMax);
+                break;
+            case J1:
+                boost::math::cyl_bessel_j_zero(1.0, 1, nIntervalsMax, std::back_inserter(bz));
+                xInt.tail(nIntervalsMax) = VectorXr::Map(&bz[0], nIntervalsMax);
+                break;
+            case NPI:
+                xInt << 1e-20, VectorXr::LinSpaced(nIntervalsMax, 1, nIntervalsMax).array() * PI;
+                break;
+        }
+        VectorXr dx = ( xInt.tail(nIntervalsMax) - xInt.head(nIntervalsMax) ).array() / 2.;
+        //  x = GaussAbscissa
+        //        dx in every row        GaussWeights+1 rows, cols = n
+        //     dx[0] dx[1] ... dx[N]       Gw[0]  Gw[0]  ... ndX
+        //     dx[0] dx[1] ... dx[N]       Gw[1]
+        MatrixXr Bxm = (dx.transpose().replicate(GaussAbscissa.size(), 1)).eval().array() *
+                 ((GaussAbscissa.replicate(1, dx.size()).array() + 1.));
+        Bxm.array() += xInt.head(Bxm.cols()).transpose().replicate( Bxm.rows(), 1 ).array();
+        Bx =  VectorXr::Map( &Bxm(0,0), Bxm.size() );
+        BJ0 = VectorXr(Bx.size());
+        BJ1 = VectorXr(Bx.size());
+        int iw = 0;
+        for (int ii=0; ii<Bx.size(); ++ii) {
+            BJ0(ii) = boost::math::cyl_bessel_j(0, Bx(ii)) * GaussWeights(iw);
+            BJ1(ii) = boost::math::cyl_bessel_j(1, Bx(ii)) * GaussWeights(iw);
+            ++iw;
+            if (iw == GaussWeights.size()) iw = 0;
+        }
+        return ;
+    # else
+        std::cerr  << "QWEKey requires Boost functionalility that is missing\n";
+    #endif
+    }		// -----  end of method QWEKey::BesselWeights  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  QWEKey
+    //      Method:  QWE
+    //--------------------------------------------------------------------------------------
+    void QWEKey::QWE ( const Real& rho ) {
+
+        // TODO, is -1 needed here?
+        int nTerms = nIntervalsMax - nDelay;// - 1;
+        int nrel = (int)(KernelManager->GetSTLVector().size());
+
+        // TODO GREMLINS LIVE IN HERE
+        MatrixXcr prev = Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic>::Zero(1, nrel);
+        for (int i=0; i<nDelay; ++i) {
+            getEyKernel(i, 0, rho);
+            prev += Zans;
+        }
+
+        // Some of these are complex
+        TS      = MatrixXcr::Zero(nrel, nTerms);
+        Tn      = VectorXi::Zero(nrel);
+        Textrap = MatrixXcr::Zero(nrel, nTerms);
+        TrelErr = MatrixXr::Zero(nrel, nTerms);
+        TabsErr = MatrixXr::Zero(nrel, nTerms);
+        VectorXi Converged = VectorXi::Zero(nrel);
+
+        // is nTerms right, 1 array shifting
+        for (int i=nDelay; i<nTerms; ++i) {
+
+            int n = i-nDelay;
+            getEyKernel(i, 0, rho);
+
+            for (int j=0; j<nrel; ++j) {
+
+                if (!Converged(j)) { //continue;
+
+                    Tn(j) = n;                            // order of the expansion
+                    TS(j,n+1) = TS(j, n) + Zans(0, j);    // working array for transformation
+
+                    /* Compute the Shanks transform using the Epsilon algorithm:
+                        Structured after Weniger (1989, p26) */
+                    /* TI - some kind ob bug here, shanks extrapolation doesn't buy much for TEM at least */
+                    Complex aux2(0);
+                    for (int k=n+1; k>0; --k) {
+                        Complex aux1 = aux2;
+                        aux2 = TS(j,k-1);
+                        Complex ddff = TS(j,k) - aux2;
+                        if (std::abs(ddff) < std::numeric_limits<Real>::min() ) {
+                            TS(j,k-1) = std::numeric_limits<Real>::max() ;
+                        } else {
+                            TS(j,k-1) = aux1 + 1./ddff;
+                        }
+
+                    }
+
+                    // The extrapolated result plus the prev integration term:
+                    Textrap(j,n) = TS(j, (n-1)%2)+prev(0, j);
+                    //Textrap(j,n) = TS(j, n%2 + 1)+prev(0, j);
+
+                    // Step 3: Analyze for convergence:
+                    if (n > 1) {
+                        TabsErr(j,n) = std::abs( Textrap(j, n) - Textrap(j, n-1));
+                        TrelErr(j,n) = TabsErr(j, n) / std::abs(Textrap(j, n)) ;
+                        Converged(j) = TrelErr(j,n) < RelTol + AbsTol/std::abs(Textrap(j,n));
+                    }
+                }
+            }
+            if ( Converged.all() == 1 ) break;
+        }
+
+        // Trim up results
+        // Clean up the T structure arrays? We can't really do this
+        // because they are fixed size, maybe see how they are used and
+        // init to zero. If they are only summed we are OK.
+        /*
+        for (int j = 0; j<nrel; ++j) {:nKernels
+            n = Tn(j);
+            T(j).extrap = T(j).extrap(1:n);
+            T(j).relErr = T(j).relErr(1:n);
+            T(j).absErr = T(j).absErr(1:n);
+        }
+        */
+        return ;
+    }		// -----  end of method QWEKey::QWE  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  QWEKey
+    //      Method:  getEyKernel
+    //--------------------------------------------------------------------------------------
+    void QWEKey::getEyKernel ( const int& i, const int& idx, const Real& rho ) {
+        int bidx = i*nQuad;
+        int nrel = (int)(KernelManager->GetSTLVector().size());
+        Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic > Zwork =
+            Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic>::Zero(nQuad, nrel);
+        for (int ik=0; ik<nQuad; ++ik) {
+            KernelManager->ComputeReflectionCoeffs( Lambda(bidx+ik), idx, rho );
+            for (int ir2=0; ir2<nrel; ++ir2) {
+                // Zwork* needed due to sign convention (e^-jwt) of FT in filter weights
+ 			    Zwork(ik, ir2) =    std::conj(KernelManager->GetSTLVector()[ir2]->RelBesselArg(Lambda(bidx+ik)));
+ 			}
+        }
+
+        Real bma  = (Intervals(i+1)-Intervals(i))/2;
+        for (int ir2=0; ir2<nrel; ++ir2) {
+            if (KernelManager->GetSTLVector()[ir2]->GetBesselOrder() == 0) {
+                Zans(0, ir2) = bma * Zwork.col(ir2).dot( BJ0.segment(bidx, nQuad) ); // / rho;
+            } else {
+                Zans(0, ir2) = bma * Zwork.col(ir2).dot( BJ1.segment(bidx, nQuad) ); // / rho;
+            }
+        }
+        // fcount += nQuad
+        return ;
+    }		// -----  end of method QWEKey::getEyKernel  -----
+
+    void QWEKey::TestPrivate(const int& N) {
+
+        //GaussQuadWeights(N);
+        //std::cout << "abscissa\n" << GaussAbscissa << std::endl;
+        //std::cout << "weights\n" << GaussWeights << std::endl;
+        BesselWeights( J1 );
+        //BesselZeros(0, N);
+        std::cout << std::scientific;
+        std::cout << "BJ0" << BJ0 << std::endl;
+        std::cout << "BJ1" << BJ1 << std::endl;
+        //std::cout << "Bess Zero\n" << xInt << std::endl;
+
+    }
+
+}		// -----  end of Lemma  name  -----
+

Modules/FDEM1D/src/UngroundedElectricDipole.cpp

@@ -0,0 +1,84 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      01/29/2014 08:55:18 AM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#include "UngroundedElectricDipole.h"
+
+namespace Lemma {
+
+    // ====================  FRIEND METHODS  =====================
+
+    std::ostream &operator<<(std::ostream &stream, const UngroundedElectricDipole &ob) {
+
+        stream << *(DipoleSource*)(&ob);
+
+        return stream;
+    }
+
+    // ====================  LIFECYCLE     =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  UngroundedElectricDipole
+    //      Method:  UngroundedElectricDipole
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    UngroundedElectricDipole::UngroundedElectricDipole (const std::string& name) : DipoleSource(name) {
+
+    }  // -----  end of method UngroundedElectricDipole::UngroundedElectricDipole  (constructor)  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  UngroundedElectricDipole
+    //      Method:  New()
+    // Description:  public constructor
+    //--------------------------------------------------------------------------------------
+    UngroundedElectricDipole* UngroundedElectricDipole::New() {
+        UngroundedElectricDipole*  Obj = new UngroundedElectricDipole("UngroundedElectricDipole");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  UngroundedElectricDipole
+    //      Method:  ~UngroundedElectricDipole
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    UngroundedElectricDipole::~UngroundedElectricDipole () {
+
+    }  // -----  end of method UngroundedElectricDipole::~UngroundedElectricDipole  (destructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  UngroundedElectricDipole
+    //      Method:  Delete
+    // Description:  public destructor
+    //--------------------------------------------------------------------------------------
+    void UngroundedElectricDipole::Delete() {
+        this->DetachFrom(this);
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  UngroundedElectricDipole
+    //      Method:  Release
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    void UngroundedElectricDipole::Release() {
+        delete this;
+    }
+
+}		// -----  end of Lemma  name  -----
+

Modules/FDEM1D/src/WireAntenna.cpp

@@ -0,0 +1,293 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     12/16/2009
+  @version  $Id: wireantenna.cpp 199 2014-12-29 19:25:20Z tirons $
+ **/
+
+#include "WireAntenna.h"
+
+namespace Lemma {
+
+    #ifdef HAVE_YAMLCPP
+    std::ostream &operator << (std::ostream &stream, const WireAntenna &ob) {
+        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
+        return stream;
+    }
+    #else
+    std::ostream &operator<<(std::ostream &stream,
+                const WireAntenna &ob) {
+
+        stream << *(LemmaObject*)(&ob);
+        stream << "Current: " << ob.Current << " [A]\n";
+        stream << "Frequencies: " << ob.Freqs.transpose() << " [Hz]\n";
+        stream << "Number of points " << ob.NumberOfPoints << "\n";
+        stream << "Number of turns " << ob.NumberOfTurns << "\n";
+
+        if (ob.NumberOfPoints) {
+            stream << "Points:\n" << ob.Points.transpose() << "\n";
+            //stream << "Dipoles used to approximate " << ob.Dipoles.size() << "\n";
+        }
+        return stream;
+    }
+    #endif
+    // ====================  LIFECYCLE     =======================
+
+    WireAntenna::WireAntenna(const std::string &name) :
+        LemmaObject(name),
+        NumberOfPoints(0), Current(1), NumberOfTurns(1) {
+    }
+
+#ifdef HAVE_YAMLCPP
+    WireAntenna::WireAntenna(const YAML::Node &node) :
+        LemmaObject(node) {
+        Points =  node["Points"].as<Vector3Xr>();
+        Freqs = node["Freqs"].as<VectorXr>();
+        NumberOfPoints = node["NumberOfPoints"].as<int>();
+        NumberOfTurns = node["NumberOfTurns"].as<int>();
+        Current = node["Current"].as<Real>();
+    }
+#endif
+
+    WireAntenna::~WireAntenna() {
+        for (unsigned int id=0; id<Dipoles.size(); ++id) {
+            Dipoles[id]->Delete();
+        }
+        Dipoles.clear();
+        if (this->NumberOfReferences != 0) {
+            throw DeleteObjectWithReferences(this);
+        }
+    }
+
+    WireAntenna* WireAntenna::New() {
+        WireAntenna* Obj = new WireAntenna("WireAntenna");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    WireAntenna* WireAntenna::Clone() {
+        WireAntenna* copy = WireAntenna::New();
+		//copy->AttachTo(copy); // NO! Attached above!
+		copy->NumberOfPoints = this->NumberOfPoints;
+		copy->Freqs = this->Freqs;
+		copy->Current = this->Current;
+		copy->NumberOfTurns = this->NumberOfTurns;
+		copy->Points = this->Points;
+		//copy->Dipoles = this->Dipoles; // no, disaster
+		return copy;
+    }
+
+    void WireAntenna::Delete() {
+        this->DetachFrom(this);
+    }
+
+    void WireAntenna::Release() {
+        delete this;
+    }
+
+
+    // ====================  ACCESS        =======================
+
+    void WireAntenna::SetNumberOfTurns(const int &nturns) {
+        this->NumberOfTurns = nturns;
+    }
+
+    int WireAntenna::GetNumberOfTurns( ) {
+        return this->NumberOfTurns;
+    }
+
+    void WireAntenna::SetNumberOfPoints(const int &np) {
+        Points.resize( Eigen::NoChange, np);
+        NumberOfPoints = np;
+    }
+
+    void WireAntenna::SetNumberOfFrequencies(const int &nfreq){
+        Freqs.resize(nfreq);
+        Freqs.setZero();
+    }
+
+    void WireAntenna::SetFrequency(const int& ifreq, const Real & freq) {
+        assert(ifreq < Freqs.size());
+        this->Freqs[ifreq] = freq;
+    }
+
+    Real WireAntenna::GetFrequency(const int& ifreq) {
+        return this->Freqs[ifreq];
+    }
+
+    int WireAntenna::GetNumberOfFrequencies() {
+        return Freqs.size();
+    }
+
+    Vector3Xr WireAntenna::GetPoints() {
+        return Points;
+    }
+
+    MatrixXr WireAntenna::GetPointsMat() {
+        return MatrixXr(Points.transpose());
+    }
+
+    void WireAntenna::SetCurrent(const Real &amps) {
+        this->Current = amps;
+    }
+
+    Real WireAntenna::GetCurrent( ) {
+        return this->Current;
+    }
+
+    void WireAntenna::SetPoint(const int &p, const Vector3r& pos) {
+
+        if (p >= 0 && p<NumberOfPoints )    {
+            Points.col(p) = pos;
+        } else {
+            throw  7;
+        }
+
+    }
+
+    void WireAntenna::SetPoint(const int &p, const Real& x, const Real& y, const Real& z) {
+
+        if (p >= 0 && p<NumberOfPoints )    {
+            Points.col(p) = Vector3r(x,y,z);
+        } else {
+            throw  7;
+        }
+
+    }
+
+
+    void WireAntenna::ApproximateWithElectricDipoles(const Real &deltai) {
+
+        // Get rid of any dipoles
+        for (unsigned int id=0; id<Dipoles.size(); ++id) {
+            Dipoles[id]->Delete();
+        }
+        Dipoles.clear();
+
+        Real Dist(0);
+        Vector3r r;
+        Vector3r p;
+
+        for (int ip=0; ip<NumberOfPoints-1; ++ip) {
+
+            Dist = (Points.col(ip+1) - Points.col(ip)).norm();
+            r = (Points.col(ip+1) - Points.col(ip))/Dist;
+
+            int nd = (int)(Dist/deltai);
+            Real add = (Dist - (Real)(nd)*deltai) / (Real)(nd);
+            Real delta = deltai + add;
+            Real scale = (Real)(NumberOfTurns)*Current;
+
+            p = Points.col(ip) + .5*delta*r;
+
+            for (Real id=0.; id<Dist-delta/2; id+=delta) {
+
+                // X dipoles
+                if (std::abs(r[0]) > 1e-6) {
+                    DipoleSource *tx = DipoleSource::New();
+                    tx->SetLocation(p);
+                    tx->SetType(GROUNDEDELECTRICDIPOLE);
+                    tx->SetPolarisation(XPOLARISATION);
+                    tx->SetFrequencies(Freqs);
+                    tx->SetMoment(scale*delta*r[0]);
+                    Dipoles.push_back(tx);
+                }
+
+                // Y dipoles
+                if (std::abs(r[1]) > 1e-6) {
+                    DipoleSource *ty = DipoleSource::New();
+                    ty->SetLocation(p);
+                    ty->SetType(GROUNDEDELECTRICDIPOLE);
+                    ty->SetPolarisation(YPOLARISATION);
+                    ty->SetFrequencies(Freqs);
+                    ty->SetMoment(scale*delta*r[1]);
+                    Dipoles.push_back(ty);
+                }
+
+                // Z dipoles
+                if (std::abs(r[2]) > 1e-6) {
+                    DipoleSource *tz = DipoleSource::New();
+                    tz->SetLocation(p);
+                    tz->SetType(GROUNDEDELECTRICDIPOLE);
+                    tz->SetPolarisation(ZPOLARISATION);
+                    tz->SetFrequencies(Freqs);
+                    tz->SetMoment(scale*delta*r[2]);
+                    Dipoles.push_back(tz);
+                }
+
+                p += delta*r;
+
+            }
+        }
+    }
+
+    // ====================  INQUIRY       =======================
+
+    int WireAntenna::GetNumberOfDipoles() {
+        return Dipoles.size();
+    }
+
+    DipoleSource* WireAntenna::GetDipoleSource(const int &dip) {
+        return this->Dipoles[dip];
+    }
+
+    #ifdef LEMMAUSEVTK
+    vtkActor* WireAntenna::GetVtkActor(const int &idip) {
+        return Dipoles[idip]->GetVtkActor();
+    }
+    #endif
+
+    #ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  WireAntenna
+    //      Method:  Serialize
+    //--------------------------------------------------------------------------------------
+    YAML::Node WireAntenna::Serialize (  ) const {
+        YAML::Node node = LemmaObject::Serialize();
+        node.SetTag( this->Name );
+        node["NumberOfPoints"] = NumberOfPoints;
+        node["NumberOfTurns"] = NumberOfTurns;
+        node["Current"] = Current;
+        node["Points"] = Points;
+        node["Freqs"] = Freqs;
+        return node;
+    }		// -----  end of method WireAntenna::Serialize  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  WireAntenna
+    //      Method:  DeSerialize
+    //--------------------------------------------------------------------------------------
+    WireAntenna* WireAntenna::DeSerialize ( const YAML::Node& node ) {
+        WireAntenna* Object = new WireAntenna(node);
+        Object->AttachTo(Object);
+        DESERIALIZECHECK( node, Object )
+        return Object ;
+    }		// -----  end of method WireAntenna::DeSerialize  -----
+
+    #endif
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  WireAntenna
+    //      Method:  IsPlanar
+    //--------------------------------------------------------------------------------------
+    bool WireAntenna::IsHorizontallyPlanar (  ) {
+        //for (int ip=0; ip<NumberOfPoints; ++ip) {
+        //   std::cout << Points(2,ip) << std::endl;
+        //}
+        if ( std::abs(Points.row(2).sum() - (NumberOfPoints*Points(2,0))) < 1e-5 ) {
+            return true ;
+        } else {
+            return false;
+        }
+    }		// -----  end of method WireAntenna::IsPlanar  -----
+
+
+}

Modules/FDEM1D/src/dipolefreqsweep.cpp

@@ -0,0 +1,345 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      01/29/2014 09:53:49 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#include <iostream>
+#include <fstream>
+#include "dipolesource.h"
+#include "layeredearthem.h"
+#include "receiverpoints.h"
+#include "emearth1d.h"
+
+#ifdef LEMMAUSEOMP
+#include "omp.h"
+#endif
+
+// For testing purposes disable VTK and run scale.sh
+//#undef LEMMAUSEVTK
+//#undef KIHALEE_EM1D
+
+#ifdef LEMMAUSEVTK
+#include "vtkRenderer.h"
+#include "vtkRenderWindow.h"
+#include "vtkRenderWindowInteractor.h"
+#include "vtkDoubleArray.h"
+#include "vtkXYPlotActor.h"
+#include "vtkXYPlotWidget.h"
+#include "vtkProperty2D.h"
+#endif
+
+#include "timer.h"
+
+using namespace Lemma;
+
+int main() {
+
+    // Do calculation
+    jsw_timer timer;
+
+    DipoleSource *dipole = DipoleSource::New();
+    dipole->SetType(MAGNETICDIPOLE);
+        dipole->SetPolarisation(0., 0.0,  1.0);
+        //dipole->SetPolarisation(XPOLARISATION);
+        //dipole->SetPolarisation(YPOLARISATION);
+        //dipole->SetPolarisation(ZPOLARISATION);
+
+        //dipole->SetMoment(1);
+        //dipole->SetLocation(1,1,-.0100328);
+        dipole->SetLocation(0., 0., -0.001);
+        //dipole->SetLocation(-2.5,1.25,0);
+        int iif=10000;
+        dipole->SetNumberOfFrequencies(iif);
+        Real w0 = 10;
+        for (int iw=0; iw<iif; ++iw) {
+            dipole->SetFrequency(iw, w0);
+            w0 += 1523.;
+        }
+
+    VectorXcr sigma(8);
+    sigma << 0., 3e-4, 5e-4, 1e-2, .5, 5e-6, .03, .04;
+    VectorXr  thick(6);
+        thick << 10 , 10 , 10 , 10 , 10 , 10;
+
+    LayeredEarthEM *earth = LayeredEarthEM::New();
+        earth->SetNumberOfLayers(8);
+        earth->SetLayerConductivity(sigma);
+        earth->SetLayerThickness(thick);
+
+    ReceiverPoints *receivers = ReceiverPoints::New();
+        Vector3r loc;
+        receivers->SetNumberOfReceivers(1);
+        loc << 150, 175, -.01;
+        receivers->SetLocation(0, loc);
+
+    // EmEarth
+    EMEarth1D  *EmEarth = EMEarth1D::New();
+        EmEarth->AttachDipoleSource(dipole);
+        EmEarth->AttachLayeredEarthEM(earth);
+        EmEarth->AttachReceiverPoints(receivers);
+        //EmEarth->SetFieldsToCalculate(BOTH);
+        EmEarth->SetFieldsToCalculate(H);
+
+        //EmEarth->SetHankelTransformMethod(GAUSSIANQUADRATURE);
+        //EmEarth->SetHankelTransformMethod(DIGITALFILTERING);
+        //EmEarth->SetHankelTransformMethod(FHTKEY201);
+        EmEarth->SetHankelTransformMethod(QWEKEY);
+
+    timer.begin();
+    EmEarth->MakeCalc3();
+    //std::cout << "H\n" << receivers->GetHfield(0)
+    //          << "End of H" << std::endl;
+    Real  lemmaTime = timer.end();
+    //std::cout << receivers->GetHfield() << std::endl;
+    std::cout << lemmaTime << "\t";
+
+    #ifdef LEMMAUSEVTK
+    vtkDataObject *_dataObjectxr = receivers->GetVtkDataObjectFreq(HFIELDREAL, 0,
+                    0, iif, XCOMPONENT, dipole->GetFrequencies());
+
+    vtkDataObject *_dataObjectxi = receivers->GetVtkDataObjectFreq(HFIELDIMAG, 0,
+                    0, iif, XCOMPONENT, dipole->GetFrequencies());
+
+    vtkDataObject *_dataObjectyr= receivers->GetVtkDataObjectFreq(HFIELDREAL, 0,
+                    0, iif, YCOMPONENT, dipole->GetFrequencies());
+
+    vtkDataObject *_dataObjectyi = receivers->GetVtkDataObjectFreq(HFIELDIMAG, 0,
+                    0, iif, YCOMPONENT, dipole->GetFrequencies());
+
+    vtkDataObject *_dataObjectzr = receivers->GetVtkDataObjectFreq(HFIELDREAL, 0,
+                    0, iif, ZCOMPONENT, dipole->GetFrequencies());
+
+    vtkDataObject *_dataObjectzi = receivers->GetVtkDataObjectFreq(HFIELDIMAG, 0,
+                    0, iif, ZCOMPONENT, dipole->GetFrequencies());
+    #endif
+
+
+//     //dipole->SetPolarisation(XPOLARISATION);
+//     //std::cout << "Fortran Calc" << std::endl;
+//     #ifdef KIHALEE_EM1D
+//     timer.begin();
+//     EmEarth->MakeCalc();
+//     Real fortranTime = timer.end();
+//     std::cout << fortranTime << "\t";
+//     std::cout << fortranTime/lemmaTime << std::endl;
+//     #endif
+
+//     #ifdef LEMMAUSEVTK
+//     vtkDataObject *_fdataObjectxr = receivers->GetVtkDataObjectFreq(HFIELDREAL, 0,
+//                     0, receivers->GetNumberOfReceivers(), XCOMPONENT, dipole->GetFrequencies());
+//
+//     vtkDataObject *_fdataObjectxi = receivers->GetVtkDataObjectFreq(HFIELDIMAG, 0,
+//                     0, receivers->GetNumberOfReceivers(), XCOMPONENT, dipole->GetFrequencies());
+//
+//     vtkDataObject *_fdataObjectyr = receivers->GetVtkDataObjectFreq(HFIELDREAL, 0,
+//                     0, receivers->GetNumberOfReceivers(), YCOMPONENT, dipole->GetFrequencies());
+//
+//     vtkDataObject *_fdataObjectyi = receivers->GetVtkDataObjectFreq(HFIELDIMAG, 0,
+//                     0, receivers->GetNumberOfReceivers(), YCOMPONENT, dipole->GetFrequencies());
+//
+//     vtkDataObject *_fdataObjectzr = receivers->GetVtkDataObjectFreq(HFIELDREAL, 0,
+//                     0, receivers->GetNumberOfReceivers(), ZCOMPONENT, dipole->GetFrequencies());
+//
+//     vtkDataObject *_fdataObjectzi = receivers->GetVtkDataObjectFreq(HFIELDIMAG, 0,
+//                     0, receivers->GetNumberOfReceivers(), ZCOMPONENT, dipole->GetFrequencies());
+//     #endif
+
+
+    #ifdef LEMMAUSEVTK
+    vtkRenderer *_ren = vtkRenderer::New();
+    vtkRenderWindow *_renwin = vtkRenderWindow::New();
+    _renwin->AddRenderer(_ren);
+
+    ///////////////////////////////////////////////
+    // X Component Plot
+    vtkXYPlotActor *_xplot = vtkXYPlotActor::New();
+    //vtkXYPlotWidget *_wplot = vtkXYPlotWidget::New();
+        // Add the datasets
+        _xplot->AddDataObjectInput( _dataObjectxr);
+        _xplot->AddDataObjectInput( _dataObjectxi);
+        //_xplot->AddDataObjectInput(_fdataObjectxr);
+        //_xplot->AddDataObjectInput(_fdataObjectxi);
+        _xplot->SetTitle("X field");
+        _xplot->SetXTitle("Depth");
+        _xplot->SetYTitle("E Field");
+        _xplot->SetXValuesToValue();
+        //_plot->SetXValuesToIndex();
+
+        // set which parts of the data object are to be used for which axis
+        _xplot->SetDataObjectXComponent(0,1);
+        _xplot->SetDataObjectYComponent(0,0);
+        _xplot->SetDataObjectXComponent(1,1);
+        _xplot->SetDataObjectYComponent(1,0);
+        _xplot->SetDataObjectXComponent(2,1);
+        _xplot->SetDataObjectYComponent(2,0);
+        _xplot->SetDataObjectXComponent(3,1);
+        _xplot->SetDataObjectYComponent(3,0);
+        _xplot->SetNumberOfXLabels(3);
+        _xplot->SetPlotColor(0,1,1,1);
+        _xplot->SetPlotColor(1,1,1,1);
+        _xplot->SetPlotColor(2,1,0,0);
+        _xplot->SetPlotColor(3,1,0,0);
+        _xplot->GetProperty()->SetLineWidth(2);
+        _xplot->GetProperty()->SetPointSize(4);
+
+        //  _plot->SetPlotPoints(0,0);
+        //  _plot->SetPlotPoints(1,0);
+        //  _plot->SetPlotPoints(2,0);
+        //  _plot->SetPlotPoints(3,0);
+
+        //  _plot->SetPlotLines(0,0);
+        //  _plot->SetPlotLines(1,0);
+        //  _plot->SetPlotLines(2,0);
+        //  _plot->SetPlotLines(3,0);
+
+        _xplot->PlotCurvePointsOff();
+        _xplot->PlotCurveLinesOff();
+        _xplot->GetPositionCoordinate()->SetValue(0.0, 0.67, 0);
+        _xplot->GetPosition2Coordinate()->SetValue(1.0, 0.33, 0);
+        //_plot->SetReverseYAxis(1); // Just flips axis, not data!
+
+    ///////////////////////////////////////////////
+    // Y Component Plot
+    vtkXYPlotActor *_yplot = vtkXYPlotActor::New();
+    //vtkXYPlotWidget *_wplot = vtkXYPlotWidget::New();
+        // Add the datasets
+        _yplot->AddDataObjectInput( _dataObjectyr);
+        _yplot->AddDataObjectInput( _dataObjectyi);
+        //_yplot->AddDataObjectInput(_fdataObjectyr);
+        //_yplot->AddDataObjectInput(_fdataObjectyi);
+        _yplot->SetTitle("Y field");
+        _yplot->SetXTitle("Depth");
+        _yplot->SetYTitle("E Field");
+        _yplot->SetXValuesToValue();
+        //_yplot->SetXValuesToIndex();
+
+        // set which parts of the data object are to be used for which axis
+        _yplot->SetDataObjectXComponent(0,1);
+        _yplot->SetDataObjectYComponent(0,0);
+        _yplot->SetDataObjectXComponent(1,1);
+        _yplot->SetDataObjectYComponent(1,0);
+        _yplot->SetDataObjectXComponent(2,1);
+        _yplot->SetDataObjectYComponent(2,0);
+        _yplot->SetDataObjectXComponent(3,1);
+        _yplot->SetDataObjectYComponent(3,0);
+        _yplot->SetNumberOfXLabels(3);
+        _yplot->SetPlotColor(0,1,1,1);
+        _yplot->SetPlotColor(1,1,1,1);
+        _yplot->SetPlotColor(2,1,0,0);
+        _yplot->SetPlotColor(3,1,0,0);
+        _yplot->GetProperty()->SetLineWidth(2);
+        _yplot->GetProperty()->SetPointSize(4);
+        _yplot->GetPositionCoordinate()->SetValue(0.00, 0.33, 0);
+        _yplot->GetPosition2Coordinate()->SetValue(1.0, 0.33, 0);
+
+        //  _plot->SetPlotPoints(0,0);
+        //  _plot->SetPlotPoints(1,0);
+        //  _plot->SetPlotPoints(2,0);
+        //  _plot->SetPlotPoints(3,0);
+
+        //  _plot->SetPlotLines(0,0);
+        //  _plot->SetPlotLines(1,0);
+        //  _plot->SetPlotLines(2,0);
+        //  _plot->SetPlotLines(3,0);
+
+        _yplot->PlotCurvePointsOff();
+        _yplot->PlotCurveLinesOff();
+        //_plot->SetReverseYAxis(1)
+
+    ///////////////////////////////////////////////
+    // Z Component Plot
+    vtkXYPlotActor *_zplot = vtkXYPlotActor::New();
+    //vtkXYPlotWidget *_wplot = vtkXYPlotWidget::New();
+        // Add the datasets
+        _zplot->AddDataObjectInput( _dataObjectzr);
+        _zplot->AddDataObjectInput( _dataObjectzi);
+        //_zplot->AddDataObjectInput(_fdataObjectzr);
+        //_zplot->AddDataObjectInput(_fdataObjectzi);
+        _zplot->SetTitle("Z field");
+        _zplot->SetXTitle("Depth");
+        _zplot->SetYTitle("E Field");
+        _zplot->SetXValuesToValue();
+        //_plot->SetXValuesToIndex();
+
+        // set which parts of the data object are to be used for which axis
+        _zplot->SetDataObjectXComponent(0,1);
+        _zplot->SetDataObjectYComponent(0,0);
+        _zplot->SetDataObjectXComponent(1,1);
+        _zplot->SetDataObjectYComponent(1,0);
+        _zplot->SetDataObjectXComponent(2,1);
+        _zplot->SetDataObjectYComponent(2,0);
+        _zplot->SetDataObjectXComponent(3,1);
+        _zplot->SetDataObjectYComponent(3,0);
+        _zplot->SetNumberOfXLabels(3);
+        _zplot->SetPlotColor(0,1,1,1);
+        _zplot->SetPlotColor(1,1,1,1);
+        _zplot->SetPlotColor(2,1,0,0);
+        _zplot->SetPlotColor(3,1,0,0);
+        _zplot->GetProperty()->SetLineWidth(2);
+        _zplot->GetProperty()->SetPointSize(4);
+        _zplot->GetPositionCoordinate()->SetValue(0.0, 0.0, 0);
+        _zplot->GetPosition2Coordinate()->SetValue(1.0, 0.33, 0);
+        //  _plot->SetPlotPoints(0,0);
+        //  _plot->SetPlotPoints(1,0);
+        //  _plot->SetPlotPoints(2,0);
+        //  _plot->SetPlotPoints(3,0);
+
+        //  _plot->SetPlotLines(0,0);
+        //  _plot->SetPlotLines(1,0);
+        //  _plot->SetPlotLines(2,0);
+        //  _plot->SetPlotLines(3,0);
+
+        _zplot->PlotCurvePointsOff();
+        _zplot->PlotCurveLinesOff();
+        //_plot->SetReverseYAxis(1)
+
+    _ren->AddActor2D(_xplot);
+    _ren->AddActor2D(_yplot);
+    _ren->AddActor2D(_zplot);
+
+    vtkRenderWindowInteractor *_iren = vtkRenderWindowInteractor::New();
+    _iren->SetRenderWindow(_renwin);
+    _iren->Initialize();
+    _renwin->Render();
+
+    //_wplot->SetXYPlotActor(_plot);
+    //_wplot->SetInteractor(_iren);
+    //_wplot->EnabledOn();
+
+    _iren->Start();
+
+    // TODO clean up you dirty whore
+//  _iren->Delete();
+//  _plot->Delete();
+//  _dataObject->Delete();
+//  _fieldData->Delete();
+//  _renwin->Delete();
+//  _ren->Delete();
+//  _xdatareal->Delete();
+//  _ydata->Delete();
+//  _depth->Delete();
+    #endif
+
+    EmEarth->Delete();
+    receivers->Delete();
+    earth->Delete();
+    dipole->Delete();
+
+    return 0;
+
+
+}

Modules/FDEM1D/src/edipole.cpp

@@ -0,0 +1,231 @@
+// ===========================================================================
+//
+//       Filename:  utsnmrinversion1d.cpp
+//
+//        Created:  10/07/2010 08:57:04 AM
+//       Compiler:  Tested with g++, icpc, and MSVC 2010
+//
+//         Author:  Trevor Irons (ti)
+//
+//   Organisation:  Colorado School of Mines (CSM)
+//                  United States Geological Survey (USGS)
+//
+//          Email:  tirons@mines.edu, tirons@usgs.gov
+//
+//  This program is free software: you can redistribute it and/or modify
+//  it under the terms of the GNU General Public License as published by
+//  the Free Software Foundation, either version 3 of the License, or
+//  (at your option) any later version.
+//
+//  This program is distributed in the hope that it will be useful,
+//  but WITHOUT ANY WARRANTY; without even the implied warranty of
+//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+//  GNU General Public License for more details.
+//
+//  You should have received a copy of the GNU General Public License
+//  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+//
+// ===========================================================================
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     10/07/2010
+  @version   0.0
+ **/
+
+#include "receiverpoints.h"
+#include "emearth1d.h"
+#include "dipolesource.h"
+
+using namespace Lemma;
+
+std::vector<Real>  readinpfile(const std::string& fname);
+
+int main(int argc, char** argv) {
+
+    std::cout <<
+    "\n"
+    << "ediple.exe Copyright (C) 2011 Broken Spoke Development, LLC\n\n"
+    << "This program is free software: you can redistribute it and/or modify\n"
+    << "it under the terms of the GNU General Public License as published by\n"
+    << "the Free Software Foundation, either version 3 of the License, or\n"
+    << "(at your option) any later version.\n\n"
+
+    << "This program is distributed in the hope that it will be useful,\n"
+    << "but WITHOUT ANY WARRANTY; without even the implied warranty of\n"
+    << "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n"
+    << "GNU General Public License for more details.\n\n"
+
+    << "You should have received a copy of the GNU General Public License\n"
+    << "along with this program.  If not, see <http://www.gnu.org/licenses/>.\n\n";
+
+    if (argc < 4) {
+        std::cout << "usage: edipole.exe  dipole.inp cond.inp points.inp \n";
+        exit(0);
+    }
+
+    std::vector<Real> Trans   = readinpfile(std::string(argv[1]));
+    std::vector<Real> CondMod = readinpfile(std::string(argv[2]));
+    std::vector<Real> Points  = readinpfile(std::string(argv[3]));
+
+    //////////////////////////////////////
+    // Define dipole source
+    DipoleSource* dipole = DipoleSource::New();
+        switch ( (int)(Trans[0]) ) {
+            case 0:
+                dipole->SetType(MAGNETICDIPOLE);
+                break;
+            case 1:
+                dipole->SetType(GROUNDEDELECTRICDIPOLE);
+                break;
+            default:
+                std::cerr << "Undefined dipole type, must be:\n"
+                     << "\t0 -> Magnetic\n"
+                     << "\t1 -> Grounded Electric\n";
+                exit(EXIT_FAILURE);
+        }
+
+        switch ( (int)(Trans[1]) ) {
+            case 0:
+                dipole->SetPolarisation(XPOLARISATION);
+                break;
+            case 1:
+                dipole->SetPolarisation(YPOLARISATION);
+                break;
+            case 2:
+                dipole->SetPolarisation(ZPOLARISATION);
+                break;
+            default:
+                std::cerr << "Undefined orientation, must be:\n"
+                          << "\t0 -> x\n"
+                          << "\t1 -> y\n"
+                          << "\t2 -> z\n";
+                exit(EXIT_FAILURE);
+        }
+        dipole->SetNumberOfFrequencies(1);
+        dipole->SetFrequency(0, Trans[2]);
+        dipole->SetLocation(Trans[3], Trans[4], Trans[5]);
+        dipole->SetMoment(Trans[6]);
+
+	// Receivers
+ 	ReceiverPoints *receivers = ReceiverPoints::New();
+        int nx = (int)Points[0];
+        int ny = (int)Points[1];
+        int nz = (int)Points[2];
+        Real ox = Points[3];
+        Real oy = Points[4];
+        Real oz = Points[5];
+     	Vector3r loc;
+        VectorXr dx(nx-1); // TODO map the dx, dy, dz vectors
+        VectorXr dy(ny-1);
+        VectorXr dz(nz-1);
+        int ip = 6;
+        int ir = 0;
+        for ( ; ip <6+nx-1; ++ip) {
+            dx[ir] = Points[ip];
+            ++ir;
+        }
+        ir = 0;
+        for ( ; ip <6+ny-1+nx-1; ++ip) {
+            dy[ir] = Points[ip];
+            ++ir;
+        }
+        ir = 0;
+        for ( ; ip <6+nz-1+ny-1+nx-1; ++ip) {
+            dz[ir] = Points[ip];
+            ++ir;
+        }
+ 		receivers->SetNumberOfReceivers(nx*ny*nz);
+ 		ir = 0;
+        Real pz  = oz;
+ 		for (int iz=0; iz<nz; ++iz) {
+ 		    Real py    =  oy;
+ 		    for (int iy=0; iy<ny; ++iy) {
+ 		        Real px    =  ox;
+ 		        for (int ix=0; ix<nx; ++ix) {
+ 			        loc << px, py, pz;
+ 			        receivers->SetLocation(ir, loc);
+ 			        if (ix < nx-1) px += dx[ix];
+ 			        ++ ir;
+     	        }
+                if (iy<ny-1) py += dy[iy];
+            }
+            if (iz<nz-1) pz += dz[iz];
+        }
+
+    ////////////////////////////////////
+    // Define model
+    LayeredEarthEM *earth = LayeredEarthEM::New();
+    VectorXcr sigma;
+    VectorXr  thick;
+ 	earth->SetNumberOfLayers(CondMod[0]+1);
+ 	sigma.resize(CondMod[0]+1); sigma(0) = 0; // airlayer
+    thick.resize(CondMod[0]-1);
+    int ilay=1;
+    for ( ; ilay/2<CondMod[0]-1; ilay+=2) {
+        sigma(ilay/2+1) =  1./CondMod[ilay];
+        thick(ilay/2) =  CondMod[ilay+1];
+    }
+    sigma(ilay/2+1) = 1./ CondMod[ilay];
+	earth->SetLayerConductivity(sigma);
+    if (thick.size() > 0) earth->SetLayerThickness(thick);
+
+	EMEarth1D  *EmEarth = EMEarth1D::New();
+		EmEarth->AttachDipoleSource(dipole);
+		EmEarth->AttachLayeredEarthEM(earth);
+		EmEarth->AttachReceiverPoints(receivers);
+		EmEarth->SetFieldsToCalculate(E);
+        EmEarth->MakeCalc3();
+
+    ////////////////////////////////////
+    // Report
+ 	std::fstream hreal("efield.dat", std::ios::out);
+    hreal << *dipole << std::endl;
+    hreal << *earth << std::endl;
+    hreal << "Right hand coordinate system, z is positive down\n\n";
+    hreal << "x[m]\ty[m]\tz[m]\tRe(Ex) [V/m]\t Im(Ex) [V/m]\tRe(Ey) [V/m]\tIm(Ey) [V/m]\tRe(Ez) [V/m] Im(Ez) [V/m]\n";
+    hreal << "\\\\ ====================================================================================================\n";
+    hreal.precision(8);
+    int i=0;
+	for (int iz=0; iz<nz; ++iz) {
+	for (int iy=0; iy<ny; ++iy) {
+	for (int ix=0; ix<nx; ++ix) {
+        hreal << receivers->GetLocation(i).transpose() << "\t";
+ 		hreal << std::real(receivers->GetEfield(0, i).transpose()[0]) << "\t";
+ 		hreal << std::imag(receivers->GetEfield(0, i).transpose()[0]) << "\t";
+ 		hreal << std::real(receivers->GetEfield(0, i).transpose()[1]) << "\t";
+ 		hreal << std::imag(receivers->GetEfield(0, i).transpose()[1]) << "\t";
+ 		hreal << std::real(receivers->GetEfield(0, i).transpose()[2]) << "\t";
+ 		hreal << std::imag(receivers->GetEfield(0, i).transpose()[2]) << "\n";
+        ++i;
+    }
+    }
+    }
+    hreal.close();
+
+    // Clean up
+    EmEarth->Delete();
+    earth->Delete();
+    receivers->Delete();
+    dipole->Delete();
+}
+
+std::vector<Real>  readinpfile(const std::string& fname) {
+    std::string buf;
+    char dump[255];
+    std::vector<Real> vals;
+    std::fstream input(fname.c_str(), std::ios::in);
+    if (input.fail()) {
+        std::cerr << "Input file " << fname << " failed to open\n";
+        exit(EXIT_FAILURE);
+    }
+    while (input >> buf) {
+        if (buf.substr(0,2) == "//") {
+            input.getline(dump, 255);
+        } else {
+            vals.push_back( atof(buf.c_str() ));
+        }
+    }
+    return vals;
+}

Modules/FDEM1D/src/emdipearth1d.cpp

@@ -0,0 +1,141 @@
+// ===========================================================================
+//
+//       Filename:  utemdipearth1d.cpp
+//
+//    Description:
+//
+//        Version:  0.0
+//        Created:  01/06/2010 04:27:56 PM
+//       Revision:  none
+//       Compiler:  g++ (c++)
+//
+//         Author:  Trevor Irons (ti)
+//
+//   Organisation:  Colorado School of Mines (CSM)
+//                  United States Geological Survey (USGS)
+//
+//          Email:  tirons@mines.edu, tirons@usgs.gov
+//
+//  This program is free software: you can redistribute it and/or modify
+//  it under the terms of the GNU General Public License as published by
+//  the Free Software Foundation, either version 3 of the License, or
+//  (at your option) any later version.
+//
+//  This program is distributed in the hope that it will be useful,
+//  but WITHOUT ANY WARRANTY; without even the implied warranty of
+//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+//  GNU General Public License for more details.
+//
+//  You should have received a copy of the GNU General Public License
+//  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+//
+// ===========================================================================
+#include "emearth1d.h"
+#include "dipolesource.h"
+#include "layeredearthem.h"
+#include "receiverpoints.h"
+
+using namespace Lemma;
+
+int main() {
+
+	// Test with a single dipole
+	DipoleSource *dipole = DipoleSource::New();
+		dipole->SetType(GROUNDEDELECTRICDIPOLE);
+		dipole->SetPolarisation(XPOLARISATION);
+		dipole->SetNumberOfFrequencies(1);
+		dipole->SetMoment(1);
+		dipole->SetFrequency(0, 4400.1000);
+		//dipole->SetPhase(0);
+		//dipole->SetLocation( (VectorXr(3) << 49, 49, -1e-4).finished() );
+		dipole->SetLocation( 49, 49, -1e-4  );
+
+
+	// Define model
+	VectorXcr sigma(2);
+		sigma << 0., 1e-3;//, .1;//, .01, .001;
+	VectorXr  thick(1);
+		thick << 10;//, 10, 10;
+
+	LayeredEarthEM *earth = LayeredEarthEM::New();
+        earth->SetNumberOfLayers(2);
+		earth->SetLayerConductivity(sigma);
+		//earth->SetLayerThickness(thick);
+
+	// Receivers
+	ReceiverPoints *receivers = ReceiverPoints::New();
+		Vector3r loc;
+		//Real ox = -5.1456;
+		//Real oy =  2.2350;
+		Real ox =    50.;
+		Real oy =    20.;
+		Real depth = 18.10;
+		Real dz = 2.6;
+		int  nz = 1;
+
+		receivers->SetNumberOfReceivers(nz);
+		int ir = 0;
+		for (int iz=0; iz<nz; ++iz) {
+			loc << ox, oy, depth;
+			receivers->SetLocation(ir, loc);
+			depth += dz;
+			++ ir;
+		}
+	//receivers->SetLocation(1, ox, oy, depth);
+
+	EMEarth1D *EmEarth = EMEarth1D::New();
+        //EmEarth->SetHankelTransformMethod(DIGITALFILTERING);
+        EmEarth->SetFieldsToCalculate(BOTH); // Fortran needs this
+		EmEarth->AttachDipoleSource(dipole);
+		EmEarth->AttachLayeredEarthEM(earth);
+		EmEarth->AttachReceiverPoints(receivers);
+
+        //dipole->SetType(ELECTRICDIPOLE);
+//         receivers->SetNumberOfReceivers(1);
+//         //for
+// 	    receivers->SetLocation(0, ox, oy, depth);
+
+
+	std::cout << "C++\n";
+	EmEarth->MakeCalc3();
+	std::cout << receivers->GetEfield(0,0) << std::endl;
+	//std::cout << receivers->GetEfield(0) << std::endl;
+	//std::cout << receivers->GetHfield(1) << std::endl;
+	//std::cout << receivers->GetEfield(1) << std::endl;
+	receivers->ClearFields();
+
+    // swap tx rx posigion
+    receivers->SetLocation(0, dipole->GetLocation());
+    dipole->SetLocation(loc);
+	EmEarth->MakeCalc3();
+	std::cout << receivers->GetEfield(0,0) << std::endl;
+
+	receivers->ClearFields();
+ #ifdef KIHALEE_EM1D
+// 	//std::cout << "\nFORTRAN\n";
+ 	EmEarth->MakeCalc();
+// 	std::cout << receivers->GetHfield(0,0) << std::endl;
+ 	std::cout << receivers->GetEfield(0,0) << std::endl;
+ #endif
+
+    dipole->Delete();
+    EmEarth->Delete();
+    receivers->Delete();
+    earth->Delete();
+
+// 	try {
+//
+// 	}
+//
+// 	// Catch exceptions
+// 	catch (NullEarth) {
+// 			std::cout << "Earth model not set dummy\n";
+// 	}
+//
+// 	catch (NullReceivers) {
+// 			std::cout << "Receivers not set dummy\n";
+// 	}
+
+	//EmEarth->TestBess();
+
+}

Modules/FDEM1D/src/emearth1d.cpp

@@ -0,0 +1,972 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     12/02/2009
+  @version  $Id: emearth1d.cpp 270 2015-08-24 15:45:41Z tirons $
+ **/
+
+#include "emearth1d.h"
+
+#ifdef LEMMAUSEOMP
+#include "omp.h"
+#endif
+
+namespace Lemma {
+
+#ifdef HAVE_YAMLCPP
+    std::ostream &operator << (std::ostream &stream, const EMEarth1D &ob) {
+        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
+        return stream;
+    }
+#else
+	std::ostream &operator<<(std::ostream &stream, const
+		EMEarth1D &ob) {
+
+		stream << *(LemmaObject*)(&ob);
+		stream << "Dipole source address: " << ob.Dipole << std::endl;
+		stream << "Wire antenna address: " << ob.Antenna << std::endl;
+		stream << *ob.Earth << std::endl;
+		stream << *ob.Receivers;
+		return stream;
+	}
+#endif
+
+#ifdef KIHALEE_EM1D
+    // Wrapper function for Fortran subroutine Em1D bi kihand
+    // Returns E or H fields (SLOW)
+    extern "C" { void em1dcall_(int &itype,   // source
+                            int     &ipol,    // source
+                            int     &nlay,    // Earth
+                            int     &nfreq,   // source
+                            int     &nfield,  // Calculator
+                            int     &nres,    // Receivers
+                            int     &jtype,   // N/A
+                            int     &jgamma,  // Controller
+                            double  &acc,     // Controller
+                            double  *dep,     // Earth
+                            std::complex<double> *sig,     // Earth
+                            double  *susl,    // Earth
+                            double  *sush,    // Earth
+                            double  *sustau,  // Earth
+                            double  *susalp,  // Earth
+                            double  *eprl,    // Earth
+                            double  *eprh,    // Earth
+                            double  *eprtau,  // Earth
+                            double  *epralp,  // Earth
+                            double  &finit,   // N/A
+                            double  &flimit,  // N/A
+                            double  &dlimit,  // N/A
+                            double  &lfinc,   // N/A
+                            double  &tx,      // Source
+                            double  &ty,      // Source
+                            double  &tz,      // Source
+                            double  *rxx,     // Receivers
+                            double  *rxy,     // Receivers
+                            double  *rxz,     // Receivers
+                            std::complex<double> *ex,      // Receivers
+                            std::complex<double> *ey,      //    |
+                            std::complex<double> *ez,      //    |
+                            std::complex<double> *hx,      //    |
+                            std::complex<double> *hy,      //    V
+                            std::complex<double> *hz );    //   ___
+    }
+#endif
+
+    // ====================  LIFECYCLE     ===================================
+
+    // TODO init large arrays here.
+    EMEarth1D::EMEarth1D(const std::string& name) : LemmaObject(name),
+            Dipole(nullptr), Earth(nullptr), Receivers(nullptr), Antenna(nullptr),
+            FieldsToCalculate(BOTH), HankelType(ANDERSON801), icalcinner(0), icalc(0)
+        //#ifdef HAVEBOOSTPROGRESS
+        //    , disp(0)
+        //#endif
+        {
+    }
+
+    EMEarth1D::~EMEarth1D() {
+        if (this->NumberOfReferences > 0)
+            throw DeleteObjectWithReferences( this );
+        DetachAll();
+    }
+
+    EMEarth1D* EMEarth1D::New() {
+        EMEarth1D * Obj = new EMEarth1D("EmEarth1D");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    void EMEarth1D::Delete() {
+        this->DetachFrom(this);
+    }
+
+    void EMEarth1D::Release() {
+        DetachAll();
+        delete this;
+    }
+
+    #ifdef HAVE_YAMLCPP
+    YAML::Node EMEarth1D::Serialize() const {
+        YAML::Node node = LemmaObject::Serialize();
+
+        node["FieldsToCalculate"] = enum2String(FieldsToCalculate);
+        node["HankelType"] = enum2String(HankelType);
+
+        //if (Dipole != NULL) node["Dipole"] = Dipole->Serialize();
+        if (Earth != NULL)     node["Earth"] = Earth->Serialize();
+        //if (Receivers != NULL) node["Receivers"] = Receivers->Serialize(); Can be huge?
+        if (Antenna != NULL)   node["Antenna"] = Antenna->Serialize();
+
+        node.SetTag( this->Name );
+
+        return node;
+    }
+    #endif
+
+    // ====================  ACCESS        ===================================
+    void EMEarth1D::AttachDipoleSource(DipoleSource *dipoleptr) {
+        if (this->Dipole != NULL) {
+            this->Dipole->DetachFrom(this);
+        }
+        dipoleptr->AttachTo(this);
+        this->Dipole = dipoleptr;
+    }
+
+    void EMEarth1D::AttachLayeredEarthEM(LayeredEarthEM *earthptr) {
+        if (this->Earth != NULL)
+            this->Earth->DetachFrom(this);
+        earthptr->AttachTo(this);
+        this->Earth = earthptr;
+    }
+
+    void EMEarth1D::AttachReceiverPoints(ReceiverPoints *recptr) {
+        if (this->Receivers != NULL) {
+            this->Receivers->DetachFrom(this);
+        }
+
+        recptr->AttachTo(this);
+        this->Receivers = recptr;
+
+        if (Receivers == NULL) {
+            std::cout << "NULL Receivers in emearth1d.cpp " << std::endl;
+            return;
+        }
+
+        if (Dipole != NULL) {
+            switch (FieldsToCalculate) {
+                case E:
+                    Receivers->SetNumberOfBinsE(Dipole->GetNumberOfFrequencies());
+                    break;
+                case H:
+                    Receivers->SetNumberOfBinsH(Dipole->GetNumberOfFrequencies());
+                    break;
+                case BOTH:
+                    Receivers->SetNumberOfBinsE(Dipole->GetNumberOfFrequencies());
+                    Receivers->SetNumberOfBinsH(Dipole->GetNumberOfFrequencies());
+                    break;
+            }
+        } else if (Antenna != NULL) {
+            switch (FieldsToCalculate) {
+                case E:
+                    Receivers->SetNumberOfBinsE(Antenna->GetNumberOfFrequencies());
+                    break;
+                case H:
+                    Receivers->SetNumberOfBinsH(Antenna->GetNumberOfFrequencies());
+                    break;
+                case BOTH:
+                    Receivers->SetNumberOfBinsE(Antenna->GetNumberOfFrequencies());
+                    Receivers->SetNumberOfBinsH(Antenna->GetNumberOfFrequencies());
+                    break;
+            }
+
+        }
+
+    }
+
+    void EMEarth1D::AttachWireAntenna(WireAntenna *antennae) {
+        if (this->Antenna != NULL) {
+            this->Antenna->DetachFrom(this);
+        }
+        antennae->AttachTo(this);
+        this->Antenna = antennae;
+    }
+
+    void EMEarth1D::SetFieldsToCalculate(const FIELDCALCULATIONS &calc) {
+        FieldsToCalculate = calc;
+    }
+
+    void EMEarth1D::SetHankelTransformMethod( const HANKELTRANSFORMTYPE &type) {
+        HankelType = type;
+    }
+
+    void EMEarth1D::Query() {
+        std::cout << "EmEarth1D::Query()" << std::endl;
+
+        std::cout << "Dipole " << Dipole;
+        if (Dipole) std::cout << *Dipole << std::endl;
+
+        std::cout << "Earth " << Earth;
+        if (Earth) std::cout << *Earth << std::endl;
+
+        std::cout << "Receivers " << Earth;
+        if (Earth) std::cout << *Receivers << std::endl;
+
+        std::cout << "Antenna " << Earth;
+        if (Antenna) std::cout << *Antenna << std::endl;
+
+        std::cout << "icalc " << icalc << std::endl;
+
+        std::cout << "icalcinner " << icalcinner << std::endl;
+    }
+
+    // ====================  OPERATIONS    ===================================
+    void EMEarth1D::DetachAll() {
+
+        if (this->Dipole != NULL){
+            this->Dipole->DetachFrom(this);
+        }
+        Dipole = NULL;
+
+        if (this->Receivers != NULL){
+            this->Receivers->DetachFrom(this);
+        }
+        Receivers = NULL;
+
+        if (this->Earth != NULL){
+            this->Earth->DetachFrom(this);
+        }
+        Earth = NULL;
+
+        if (this->Antenna != NULL){
+            this->Antenna->DetachFrom(this);
+        }
+        Antenna = NULL;
+    }
+
+    void EMEarth1D::CalculateWireAntennaFields(bool progressbar) {
+
+        #ifdef HAVEBOOSTPROGRESS
+        boost::progress_display *disp;
+        #endif
+
+        if (Earth == NULL) {
+            throw NullEarth();
+        }
+        if (Receivers == NULL) {
+            throw NullReceivers();
+        }
+        if (Antenna == NULL) {
+            throw NullAntenna();
+        }
+        if (Dipole != NULL) {
+            throw DipoleSourceSpecifiedForWireAntennaCalc();
+        }
+
+        Receivers->ClearFields();
+
+        // Check to make sure Receivers are set up for all calculations
+        switch(FieldsToCalculate) {
+            case E:
+                if (Receivers->NumberOfBinsE != Antenna->GetNumberOfFrequencies())
+                    Receivers->SetNumberOfBinsE(Antenna->GetNumberOfFrequencies());
+                break;
+            case H:
+                if (Receivers->NumberOfBinsH != Antenna->GetNumberOfFrequencies())
+                    Receivers->SetNumberOfBinsH(Antenna->GetNumberOfFrequencies());
+                break;
+            case BOTH:
+                if (Receivers->NumberOfBinsH != Antenna->GetNumberOfFrequencies())
+                    Receivers->SetNumberOfBinsH(Antenna->GetNumberOfFrequencies());
+                if (Receivers->NumberOfBinsE != Antenna->GetNumberOfFrequencies())
+                    Receivers->SetNumberOfBinsE(Antenna->GetNumberOfFrequencies());
+                break;
+        }
+
+        if (Antenna->GetName() == std::string("PolygonalWireAntenna") || Antenna->GetName() == std::string("TEMTransmitter") ) {
+
+            icalc += 1;
+
+            // Check to see if they are all on a plane? If so we can do this fast
+            /* TODO FIX THIS ISSUES */
+            if (Antenna->IsHorizontallyPlanar() && HankelType == ANDERSON801) {
+                //std::cout << "Lag baby lag" << std::endl;
+                for (int ifreq=0; ifreq<Antenna->GetNumberOfFrequencies();++ifreq) {
+                    //std::cout << "Num Recs" <<  Receivers->GetNumberOfReceivers() << std::endl;
+                    Real wavef = 2.*PI* Antenna->GetFrequency(ifreq);
+                    #ifdef LEMMAUSEOMP
+                    #pragma omp parallel
+                    {
+                    #endif
+                    Hankel2* Hankel = Hankel2::New();
+                    #ifdef LEMMAUSEOMP
+                    #pragma omp for schedule(static, 1)
+                    #endif
+                    for (int irec=0; irec<Receivers->GetNumberOfReceivers(); ++irec) {
+                    //for (int irec=0; irec<2; ++irec) { // TODO FIXME BELO
+                        PolygonalWireAntenna *AntCopy = static_cast<PolygonalWireAntenna*>(this->Antenna)->Clone();
+                        SolveLaggedTxRxPair(irec, Hankel, wavef, ifreq, AntCopy);
+                        AntCopy->Delete();
+                        //exit(0);
+                    }
+                    //Receivers->ClearFields(); // FIXME DEBUG TODO
+                    Hankel->Delete();
+                    #ifdef LEMMAUSEOMP
+                    }
+                    #endif
+                }
+            } else
+            if (Receivers->GetNumberOfReceivers() > Antenna->GetNumberOfFrequencies()) {
+
+                //std::cout << "freq parallel #1" << std::endl;
+                //** Progress display bar for long calculations */
+                #ifdef HAVEBOOSTPROGRESS
+                if (progressbar) {
+                    disp = new boost::progress_display( Receivers->GetNumberOfReceivers()*Antenna->GetNumberOfFrequencies() );
+                }
+                #endif
+
+                // parallelise across receivers
+                #ifdef LEMMAUSEOMP
+                #pragma omp parallel
+                #endif
+                { // OpenMP Parallel Block
+                    // Since these antennas change we need a local copy for each
+                    // thread.
+                    PolygonalWireAntenna *AntCopy =
+                            static_cast<PolygonalWireAntenna*>(this->Antenna)->Clone();
+
+                    HankelTransform* Hankel;
+                    switch (HankelType) {
+                        case ANDERSON801:
+                            Hankel = Hankel2::New();
+                            break;
+                        case CHAVE:
+                            Hankel = HankelTransformGaussianQuadrature::New();
+                            break;
+                        case FHTKEY201:
+                            Hankel = FHTKey::New();
+                            break;
+                        case FHTKEY101:
+                            Hankel = FHTKey101::New();
+                            break;
+                        case FHTKEY51:
+                            Hankel = FHTKey51::New();
+                            break;
+                        case QWEKEY:
+                            Hankel = QWEKey::New();
+                            break;
+                        default:
+                            std::cerr << "Hankel transform cannot be created\n";
+                            exit(EXIT_FAILURE);
+                    }
+
+                    //for (int irec=tid; irec<Receivers->GetNumberOfReceivers(); irec+=nthreads) {
+                    #ifdef LEMMAUSEOMP
+                    #pragma omp for schedule(static, 1) //nowait
+                    #endif
+                    for (int irec=0; irec<Receivers->GetNumberOfReceivers(); ++irec) {
+                        if (!Receivers->GetMask(irec)) {
+                            AntCopy->ApproximateWithElectricDipoles(Receivers->GetLocation(irec));
+                            for (int idip=0; idip<AntCopy->GetNumberOfDipoles(); ++idip) {
+                                DipoleSource* tDipole = AntCopy->GetDipoleSource(idip);
+                                //#ifdef LEMMAUSEOMP
+                                //#pragma omp for schedule(static, 1)
+                                //#endif
+                                for (int ifreq=0; ifreq<tDipole->GetNumberOfFrequencies();
+                                        ++ifreq) {
+                                    // Propogation constant in free space
+                                    Real wavef   = tDipole->GetAngularFrequency(ifreq) *
+                                          std::sqrt(MU0*EPSILON0);
+                                    SolveSingleTxRxPair(irec, Hankel, wavef, ifreq, tDipole);
+                                } // freq loop
+                            } // dipole loop
+                        } // mask
+                        //std::cout << "Normal Path\n";
+                        //std::cout << Receivers->GetHfield(0, irec) << std::endl;
+                        //if (irec == 1) exit(0);
+                        #ifdef HAVEBOOSTPROGRESS
+                        if (progressbar) ++(*disp);
+                        #endif
+                    } // receiver loop
+                    Hankel->Delete();
+                    AntCopy->Delete();
+                } // OMP_PARALLEL BLOCK
+            } else if (Antenna->GetNumberOfFrequencies() > 8) {
+                // parallel across frequencies
+                //std::cout << "freq parallel #2" << std::endl;
+                for (int irec=0; irec<Receivers->GetNumberOfReceivers(); ++irec) {
+                    if (!Receivers->GetMask(irec)) {
+                        static_cast<PolygonalWireAntenna*>(Antenna)->
+                            ApproximateWithElectricDipoles(Receivers->GetLocation(irec));
+                        #ifdef LEMMAUSEOMP
+                        #pragma omp parallel
+                        #endif
+                        { // OpenMP Parallel Block
+
+                            HankelTransform* Hankel;
+                            switch (HankelType) {
+                                case ANDERSON801:
+                                    Hankel = Hankel2::New();
+                                    break;
+                                case CHAVE:
+                                    Hankel = HankelTransformGaussianQuadrature::New();
+                                    break;
+                                case FHTKEY201:
+                                    Hankel = FHTKey::New();
+                                    break;
+                                case FHTKEY101:
+                                    Hankel = FHTKey101::New();
+                                    break;
+                                case FHTKEY51:
+                                    Hankel = FHTKey51::New();
+                                    break;
+                                case QWEKEY:
+                                    Hankel = QWEKey::New();
+                                    break;
+                                default:
+                                    std::cerr << "Hankel transform cannot be created\n";
+                                    exit(EXIT_FAILURE);
+                            }
+                            #ifdef LEMMAUSEOMP
+                            #pragma omp for schedule(static, 1)
+                            #endif
+                            for (int ifreq=0; ifreq<Antenna->GetNumberOfFrequencies(); ++ifreq) {
+                                for (int idip=0; idip<Antenna->GetNumberOfDipoles(); ++idip) {
+                                    DipoleSource* tDipole = Antenna->GetDipoleSource(idip);
+                                    // Propogation constant in free space
+                                    Real wavef   = tDipole->GetAngularFrequency(ifreq) *
+                                          std::sqrt(MU0*EPSILON0);
+                                    SolveSingleTxRxPair(irec, Hankel, wavef,
+                                                    ifreq, tDipole);
+                                } // dipole loop
+                            } // frequency loop
+                            Hankel->Delete();
+                        } // OMP_PARALLEL BLOCK
+                    } // mask loop
+                    #ifdef HAVEBOOSTPROGRESS
+                    //if (Receivers->GetNumberOfReceivers() > 100) {
+                    //    ++ disp;
+                    //}
+                    #endif
+                } // receiver loop
+                //std::cout << "End freq parallel " << std::endl;
+            } // Frequency Parallel
+              else {
+                //std::cout << "parallel across #3 " << std::endl;
+                for (int irec=0; irec<Receivers->GetNumberOfReceivers(); ++irec) {
+                    if (!Receivers->GetMask(irec)) {
+
+                        static_cast<PolygonalWireAntenna*>(Antenna)->
+                            ApproximateWithElectricDipoles(Receivers->GetLocation(irec));
+//                         std::cout << "Not Masked " << std::endl;
+//                         std::cout << "n Freqs " << Antenna->GetNumberOfFrequencies() << std::endl;
+//                         std::cout << "n Dipoles " << Antenna->GetNumberOfDipoles() << std::endl;
+//                         if ( !Antenna->GetNumberOfDipoles() ) {
+//                             std::cout << "NO DIPOLES!!!!!!!!!!!!!!!!!!!!!!!!!!\n";
+// //                            std::cout << "rec location " << Receivers->GetLocation(irec) << std::endl;
+// //                        }
+
+                        #ifdef LEMMAUSEOMP
+                        #pragma omp parallel
+                        #endif
+                        { // OpenMP Parallel Block
+                            HankelTransform* Hankel;
+                            switch (HankelType) {
+                                case ANDERSON801:
+                                    Hankel = Hankel2::New();
+                                    break;
+                                case CHAVE:
+                                    Hankel = HankelTransformGaussianQuadrature::New();
+                                    break;
+                                case FHTKEY201:
+                                    Hankel = FHTKey::New();
+                                    break;
+                                case FHTKEY101:
+                                    Hankel = FHTKey101::New();
+                                    break;
+                                case FHTKEY51:
+                                    Hankel = FHTKey51::New();
+                                    break;
+                                case QWEKEY:
+                                    Hankel = QWEKey::New();
+                                    break;
+                                default:
+                                    std::cerr << "Hankel transform cannot be created\n";
+                                    exit(EXIT_FAILURE);
+                            }
+                            for (int ifreq=0; ifreq<Antenna->GetNumberOfFrequencies(); ++ifreq) {
+                                #ifdef LEMMAUSEOMP
+                                #pragma omp for schedule(static, 1)
+                                #endif
+                                for (int idip=0; idip<Antenna->GetNumberOfDipoles(); ++idip) {
+                                    //#pragma omp critical
+                                    //{
+                                    //cout << "idip=" << idip << "\tthread num=" << omp_get_thread_num() << '\n';
+                                    //}
+                                    DipoleSource* tDipole = Antenna->GetDipoleSource(idip);
+                                    // Propogation constant in free space
+                                    Real wavef   = tDipole->GetAngularFrequency(ifreq) *
+                                          std::sqrt(MU0*EPSILON0);
+                                    SolveSingleTxRxPair(irec, Hankel, wavef, ifreq, tDipole);
+                                } // dipole loop
+                            } // frequency loop
+                            Hankel->Delete();
+                        } // OMP_PARALLEL BLOCK
+                    } // mask loop
+                    #ifdef HAVEBOOSTPROGRESS
+                    //if (Receivers->GetNumberOfReceivers() > 100) {
+                    //    ++ disp;
+                    //}
+                    #endif
+                } // receiver loop
+           } // Polygonal parallel logic
+        } else {
+             std::cerr << "Lemma with WireAntenna class is currently broken"
+                  << " fix or use PolygonalWireAntenna\n" << std::endl;
+             exit(EXIT_FAILURE);
+            // TODO, getting wrong answer, curiously worKernel->GetKs() with MakeCalc, maybe
+            // a threading issue, use SolveSingleTxRxPair maype instead of call
+            // to MakeCalc3? !!!
+            for (int idip=0; idip<Antenna->GetNumberOfDipoles(); ++idip) {
+                this->Dipole = Antenna->GetDipoleSource(idip);
+                MakeCalc3();
+                //++disp;
+            }
+            this->Dipole = NULL;
+        }
+
+        #ifdef HAVEBOOSTPROGRESS
+        if (progressbar) {
+            delete disp;
+        }
+        #endif
+    }
+
+    #ifdef KIHALEE_EM1D
+    void EMEarth1D::MakeCalc() {
+
+        int itype;       // 1 = elec, 2 = mag
+        switch (this->Dipole->GetDipoleSourceType()) {
+            case (GROUNDEDELECTRICDIPOLE) :
+                itype = 1;
+                break;
+            case (MAGNETICDIPOLE) :
+                itype = 2;
+                break;
+            case (UNGROUNDEDELECTRICDIPOLE) :
+                std::cerr << "Fortran routine cannot calculate ungrounded"
+                             "electric dipole\n";
+            default:
+                throw NonValidDipoleType();
+        }
+
+        int ipol ;
+        Vector3r Pol = this->Dipole->GetPolarisation();
+        if (std::abs(Pol[0]-1) < 1e-5) {
+            ipol = 1;
+        } else if (std::abs(Pol[1]-1) < 1e-5) {
+            ipol = 2;
+        } else if (std::abs(Pol[2]-1) < 1e-5) {
+            ipol = 3;
+        } else {
+            std::cerr << "Fortran routine cannot calculate arbitrary "
+                             "dipole polarisation, set to x, y, or z\n";
+        }
+
+        int nlay   =  Earth->GetNumberOfNonAirLayers();
+
+        if (nlay > MAXLAYERS) {
+            std::cerr << "FORTRAN CODE CAN ONLY HANDLE " << MAXLAYERS
+                      << " LAYERS\n";
+            throw  EarthModelWithMoreThanMaxLayers();
+        }
+
+        int nfreq  = 1;     // number of freqs
+
+        int nfield;     // field output 1 = elec, 2 = mag, 3 = both
+        switch (FieldsToCalculate) {
+            case E:
+                nfield = 1;
+                break;
+            case H:
+                nfield = 2;
+                break;
+            case BOTH:
+                nfield = 3;
+                break;
+            default:
+                throw 7;
+        }
+
+        int nres   = Receivers->GetNumberOfReceivers();
+        int jtype  = 3;     // form ouf output,
+                            // 1 = horizontal,
+                            // 2 = down hole,
+                            // 3 = freq sounding
+                            // 4 = down hole logging
+
+        int jgamma = 0;     // Units 0 = MKS (H->A/m and E->V/m)
+                            //       1 = h->Gammas   E->V/m
+
+        double acc = 0.;    // Tolerance
+
+        // TODO, fix FORTRAN calls so these arrays can be nlay long, not
+        // MAXLAYERS.
+
+        // Model Parameters
+        double *dep    = new double[MAXLAYERS];
+        dep[0] = 0.;          // We always say air starts at 0
+        for (int ilay=1; ilay<Earth->GetNumberOfLayers(); ++ilay) {
+            dep[ilay] = dep[ilay-1] + Earth->GetLayerThickness(ilay);
+            //std::cout << "Depth " << dep[ilay] << std::endl;
+        }
+
+        std::complex<double> *sig = new std::complex<double> [MAXLAYERS];
+        for (int ilay=1; ilay<=nlay; ++ilay) {
+            sig[ilay-1] = (std::complex<double>)(Earth->GetLayerConductivity(ilay));
+        }
+
+        // TODO, pass these into Fortran call, and return Cole-Cole model
+        // parameters. Right now this does nothing
+        //std::complex<double> *sus   = new std::complex<double>[MAXLAYERS];
+        //std::complex<double> *epr   = new std::complex<double>[MAXLAYERS];
+
+        // Cole-Cole model stuff
+        double *susl   = new double[MAXLAYERS];
+        for (int ilay=1; ilay<=nlay; ++ilay) {
+            susl[ilay-1] = Earth->GetLayerLowFreqSusceptibility(ilay);
+        }
+
+        double *sush   = new double[MAXLAYERS];
+        for (int ilay=1; ilay<=nlay; ++ilay) {
+            sush[ilay-1] = Earth->GetLayerHighFreqSusceptibility(ilay);
+        }
+
+        double *sustau = new double[MAXLAYERS];
+        for (int ilay=1; ilay<=nlay; ++ilay) {
+            sustau[ilay-1] = Earth->GetLayerTauSusceptibility(ilay);
+        }
+
+        double *susalp = new double[MAXLAYERS];
+        for (int ilay=1; ilay<=nlay; ++ilay) {
+            susalp[ilay-1] = Earth->GetLayerBreathSusceptibility(ilay);
+        }
+
+        double *eprl   = new double[MAXLAYERS];
+        for (int ilay=1; ilay<=nlay; ++ilay) {
+            eprl[ilay-1] = Earth->GetLayerLowFreqPermitivity(ilay);
+        }
+
+        double *eprh   = new double[MAXLAYERS];
+        for (int ilay=1; ilay<=nlay; ++ilay) {
+            eprh[ilay-1] = Earth->GetLayerHighFreqPermitivity(ilay);
+        }
+
+        double *eprtau = new double[MAXLAYERS];
+        for (int ilay=1; ilay<=nlay; ++ilay) {
+            eprtau[ilay-1] = Earth->GetLayerTauPermitivity(ilay);
+        }
+
+        double *epralp = new double[MAXLAYERS];
+        for (int ilay=1; ilay<=nlay; ++ilay) {
+            epralp[ilay-1] = Earth->GetLayerBreathPermitivity(ilay);
+        }
+
+        // Freq stuff
+        double finit  = Dipole->GetFrequency(0); //(1000);   // Starting freq
+        double flimit = Dipole->GetFrequency(0); //(1000);   // max freq
+        double dlimit = Dipole->GetFrequency(0); //(1000);   // difusion limit
+        double lfinc(1);       // no. freq per decade
+
+        // tx location jtype != 4
+        double txx = Dipole->GetLocation(0); // (0.);
+        double txy = Dipole->GetLocation(1); // (0.);
+        double txz = Dipole->GetLocation(2); // (0.);
+
+        // rx position
+        // TODO, fix Fortran program to not waste this memory
+        // maybe
+        const int MAXREC = 15;
+        double *rxx = new double [MAXREC];
+        double *rxy = new double [MAXREC];
+        double *rxz = new double [MAXREC];
+
+        std::complex<double> *ex = new std::complex<double>[MAXREC];
+        std::complex<double> *ey = new std::complex<double>[MAXREC];
+        std::complex<double> *ez = new std::complex<double>[MAXREC];
+
+        std::complex<double> *hx = new std::complex<double>[MAXREC];
+        std::complex<double> *hy = new std::complex<double>[MAXREC];
+        std::complex<double> *hz = new std::complex<double>[MAXREC];
+
+        int nres2 = MAXREC;
+        int ii=0;
+
+        for (ii=0; ii<nres-MAXREC; ii+=MAXREC) {
+
+            for (int ir=0; ir<MAXREC; ++ir) {
+                //Vector3r pos = Receivers->GetLocation(ii+ir);
+                rxx[ir] = Receivers->GetLocation(ii+ir)[0];
+                rxy[ir] = Receivers->GetLocation(ii+ir)[1];
+                rxz[ir] = Receivers->GetLocation(ii+ir)[2];
+            }
+
+            em1dcall_(itype, ipol, nlay, nfreq, nfield, nres2, jtype,
+                  jgamma, acc, dep, sig, susl, sush, sustau, susalp,
+                  eprl, eprh, eprtau, epralp, finit, flimit, dlimit,
+                  lfinc, txx, txy, txz, rxx, rxy, rxz, ex, ey, ez,
+                  hx, hy, hz);
+
+            // Scale By Moment
+            for (int ir=0; ir<MAXREC; ++ir) {
+
+                ex[ir] *= Dipole->GetMoment();
+                ey[ir] *= Dipole->GetMoment();
+                ez[ir] *= Dipole->GetMoment();
+
+                hx[ir] *= Dipole->GetMoment();
+                hy[ir] *= Dipole->GetMoment();
+                hz[ir] *= Dipole->GetMoment();
+
+                // Append values instead of setting them
+                this->Receivers->AppendEfield(0, ii+ir, (Complex)(ex[ir]),
+                                                        (Complex)(ey[ir]),
+                                                        (Complex)(ez[ir]) );
+                this->Receivers->AppendHfield(0, ii+ir, (Complex)(hx[ir]),
+                                                        (Complex)(hy[ir]),
+                                                        (Complex)(hz[ir]) );
+            }
+        }
+
+        //ii += MAXREC;
+        nres2 = 0;
+        // Perform last positions
+        for (int ir=0; ir<nres-ii; ++ir) {
+            rxx[ir] = Receivers->GetLocation(ii+ir)[0];
+            rxy[ir] = Receivers->GetLocation(ii+ir)[1];
+            rxz[ir] = Receivers->GetLocation(ii+ir)[2];
+            ++nres2;
+        }
+
+        em1dcall_(itype, ipol, nlay, nfreq, nfield, nres2, jtype,
+              jgamma, acc, dep, sig, susl, sush, sustau, susalp,
+              eprl, eprh, eprtau, epralp, finit, flimit, dlimit,
+              lfinc, txx, txy, txz, rxx, rxy, rxz, ex, ey, ez,
+              hx, hy, hz);
+
+        // Scale By Moment
+        for (int ir=0; ir<nres-ii; ++ir) {
+
+            ex[ir] *= Dipole->GetMoment();
+            ey[ir] *= Dipole->GetMoment();
+            ez[ir] *= Dipole->GetMoment();
+
+            hx[ir] *= Dipole->GetMoment();
+            hy[ir] *= Dipole->GetMoment();
+            hz[ir] *= Dipole->GetMoment();
+
+            // Append values instead of setting them
+            this->Receivers->AppendEfield(0, ii+ir, (Complex)(ex[ir]),
+                                                    (Complex)(ey[ir]),
+                                                    (Complex)(ez[ir]) );
+            this->Receivers->AppendHfield(0, ii+ir, (Complex)(hx[ir]),
+                                                    (Complex)(hy[ir]),
+                                                    (Complex)(hz[ir]) );
+
+        }
+
+        delete [] sig;
+        delete [] dep;
+
+        //delete [] sus;
+        //delete [] epr;
+
+        delete [] susl;
+        delete [] sush;
+        delete [] susalp;
+        delete [] sustau;
+
+        delete [] eprl;
+        delete [] eprh;
+        delete [] epralp;
+        delete [] eprtau;
+
+        delete [] rxx;
+        delete [] rxy;
+        delete [] rxz;
+
+        delete [] ex;
+        delete [] ey;
+        delete [] ez;
+
+        delete [] hx;
+        delete [] hy;
+        delete [] hz;
+
+    }
+#endif
+
+
+    void EMEarth1D::SolveSingleTxRxPair (const int &irec,
+                   HankelTransform *Hankel, const Real &wavef, const int &ifreq,
+                   DipoleSource *tDipole) {
+        ++icalcinner;
+
+        Real rho = (Receivers->GetLocation(irec).head<2>() - tDipole->GetLocation().head<2>()).norm();
+
+        tDipole->SetKernels(ifreq, FieldsToCalculate, Receivers, irec, Earth);
+        Hankel->ComputeRelated( rho, tDipole->GetKernelManager() );
+        tDipole->UpdateFields( ifreq,  Hankel, wavef );
+    }
+
+    void EMEarth1D::SolveLaggedTxRxPair(const int &irec, Hankel2* Hankel,
+                    const Real &wavef, const int &ifreq, PolygonalWireAntenna* antenna) {
+
+        antenna->ApproximateWithElectricDipoles(Receivers->GetLocation(irec));
+
+        // Determine the min and max arguments
+        Real rhomin = 1e9;
+        Real rhomax = 1e-9;
+        for (int idip=0; idip<antenna->GetNumberOfDipoles(); ++idip) {
+            DipoleSource* tDipole = antenna->GetDipoleSource(idip);
+            Real rho = (Receivers->GetLocation(irec).head<2>() - tDipole->GetLocation().head<2>()).norm();
+            rhomin = std::min(rhomin, rho);
+            rhomax = std::max(rhomax, rho);
+        }
+        //std::cout << "rhomin\t" << rhomin << "\trhomax" << rhomax << std::endl;
+
+        // Determine number of lagged convolutions to do
+        // TODO, can Hankel2 adjust the lagg spacing safely?
+        int nlag = 1; // We need an extra for some reason for stability
+        Real lrho ( 1.01* rhomax );
+        while ( lrho > rhomin ) {
+            nlag += 1;
+            lrho *= Hankel->GetABSER();
+        }
+
+        //int nlag = rhomin
+        DipoleSource* tDipole = antenna->GetDipoleSource(0);
+        tDipole->SetKernels(ifreq, FieldsToCalculate, Receivers, irec, Earth);
+
+        // Instead we should pass the antenna into this so that Hankel hass all the rho arguments...
+        Hankel->ComputeLaggedRelated( 1.01* rhomax, nlag, tDipole->GetKernelManager() );
+
+        //std::cout << Hankel->GetAnswer() << std::endl;
+        //std::cout << Hankel->GetArg() << std::endl;
+
+
+        // Sort the dipoles by rho
+
+        for (int idip=0; idip<antenna->GetNumberOfDipoles(); ++idip) {
+        //for (int idip=0; idip<1; ++idip) {
+            DipoleSource* tDipole = antenna->GetDipoleSource(idip);
+            tDipole->SetKernels(ifreq, FieldsToCalculate, Receivers, irec, Earth);
+            // Pass Hankel2 a message here so it knows which one to return in Zgauss!
+            Real rho = (Receivers->GetLocation(irec).head<2>() - tDipole->GetLocation().head<2>()).norm();
+            //std::cout << " in Lagged " <<  rho << "\t" << rhomin << "\t" << rhomax << std::endl;
+            Hankel->SetLaggedArg( rho );
+            //std::cout << "out Lagged" << std::endl;
+            tDipole->UpdateFields( ifreq,  Hankel, wavef );
+        }
+        //std::cout << "Spline\n";
+        //std::cout << Receivers->GetHfield(0, irec) << std::endl;
+    }
+
+    //////////////////////////////////////////////////////////
+    // Thread safe OO Reimplimentation of KiHand's
+    // EM1DNEW.for programme
+    void EMEarth1D::MakeCalc3() {
+
+        if ( Dipole == NULL ) throw NullDipoleSource();
+
+        if (Earth == NULL) throw NullEarth();
+
+        if (Receivers == NULL) throw NullReceivers();
+
+        #ifdef LEMMAUSEOMP
+        #pragma omp parallel
+        #endif
+        { // OpenMP Parallel Block
+
+            #ifdef LEMMAUSEOMP
+            int tid = omp_get_thread_num();
+            int nthreads = omp_get_num_threads();
+            #else
+            int tid=0;
+            int nthreads=1;
+            #endif
+
+            DipoleSource* tDipole = Dipole->Clone();
+
+            HankelTransform* Hankel;
+            switch (HankelType) {
+                case ANDERSON801:
+                    Hankel = Hankel2::New();
+                    break;
+                case CHAVE:
+                    Hankel = HankelTransformGaussianQuadrature::New();
+                    break;
+                case FHTKEY201:
+                    Hankel = FHTKey::New();
+                    break;
+                case FHTKEY101:
+                    Hankel = FHTKey101::New();
+                    break;
+                case FHTKEY51:
+                    Hankel = FHTKey51::New();
+                    break;
+                case QWEKEY:
+                    Hankel = QWEKey::New();
+                    break;
+                default:
+                    std::cerr << "Hankel transform cannot be created\n";
+                    exit(EXIT_FAILURE);
+            }
+
+            if ( tDipole->GetNumberOfFrequencies() < Receivers->GetNumberOfReceivers() ) {
+                for (int ifreq=0; ifreq<tDipole->GetNumberOfFrequencies(); ++ifreq) {
+                    // Propogation constant in free space being input to Hankel
+                    Real wavef   = tDipole->GetAngularFrequency(ifreq) * std::sqrt(MU0*EPSILON0);
+                    for (int irec=tid; irec<Receivers->GetNumberOfReceivers(); irec+=nthreads) {
+                        SolveSingleTxRxPair(irec, Hankel, wavef, ifreq, tDipole);
+                    }
+                }
+            } else {
+                for (int irec=0; irec<Receivers->GetNumberOfReceivers(); ++irec) {
+                    for (int ifreq=tid; ifreq<tDipole->GetNumberOfFrequencies(); ifreq+=nthreads) {
+                        // Propogation constant in free space being input to Hankel
+                        Real wavef   = tDipole->GetAngularFrequency(ifreq) * std::sqrt(MU0*EPSILON0);
+                        SolveSingleTxRxPair(irec, Hankel, wavef, ifreq, tDipole);
+                    }
+                }
+            }
+
+            tDipole->Delete();
+            Hankel->Delete();
+
+        } // OpenMP Parallel Block
+    }
+
+    NullReceivers::NullReceivers() :
+        runtime_error("NULL RECEIVERS") {}
+
+    NullAntenna::NullAntenna() :
+        runtime_error("NULL ANTENNA") {}
+
+    NullInstrument::NullInstrument(LemmaObject* ptr) :
+        runtime_error("NULL INSTRUMENT") {
+        std::cout << "Thrown by instance of "
+                  << ptr->GetName() << std::endl;
+    }
+
+    DipoleSourceSpecifiedForWireAntennaCalc::
+        DipoleSourceSpecifiedForWireAntennaCalc() :
+        runtime_error("DIPOLE SOURCE SPECIFIED FOR WIRE ANTENNA CALC"){}
+
+} // end of Lemma Namespace

Modules/FDEM1D/src/femforward.cpp

@@ -0,0 +1,199 @@
+// ===========================================================================
+// 
+//       Filename:  utfemforward.cpp
+// 
+//    Description:  
+// 
+//        Version:  0.0
+//        Created:  01/15/2013 12:11:34 PM
+//       Revision:  none
+//       Compiler:  Tested with g++ 
+// 
+//         Author:  M. Andy Kass (MAK)
+//
+//   Organisation:  Broken Spoke Development, LLC
+//                  
+//
+//          Email:  mkass@numericalgeo.com
+// 
+//  This program is free software: you can redistribute it and/or modify
+//  it under the terms of the GNU General Public License as published by
+//  the Free Software Foundation, either version 3 of the License, or
+//  (at your option) any later version.
+//
+//  This program is distributed in the hope that it will be useful,
+//  but WITHOUT ANY WARRANTY; without even the implied warranty of
+//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+//  GNU General Public License for more details.
+//
+//  You should have received a copy of the GNU General Public License
+//  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+//
+// ===========================================================================
+
+#include <time.h>
+#include "Lemma"
+#include "banner.h"
+
+using namespace Lemma;
+
+#ifdef LEMMAUSEVTK
+#include "matplot.h"
+using namespace matplot;
+#endif
+
+int main() {
+
+	clock_t launch = clock();
+
+	// Banner display
+	std::string name;
+	std::string version;
+	std::string usage;
+	name = "FEM Forward Modeller - 1D ";
+	version = "1.0alpha";
+	usage = "utfemforward [inputfile]";
+	banner(name,version,usage);
+
+	time_t curr = time(0);
+	std::cout << std::endl << "  Start time: " << ctime(&curr) << std::endl;
+
+	// Define some objects
+	DipoleSource* Trans = DipoleSource::New();
+	ReceiverPoints* Receivers = ReceiverPoints::New();
+	LayeredEarthEM* Earth = LayeredEarthEM::New();
+
+
+
+	// SINGLE SOUNDING
+
+	// Create new data object to receive forward model
+	DataFEM* modelledData = DataFEM::New();
+
+	// Create instrument object
+	InstrumentFem* theinstrument = InstrumentFem::New();	
+
+	// Set up EMEarthModel
+	Earth->SetNumberOfLayers(5);
+	Earth->SetLayerConductivity((VectorXcr(5) << 0.,1.e-4,1.e-2,
+		1.e-4,1.e-6).finished());
+	Earth->SetLayerThickness((VectorXr(3) << 20.,5.,50.).finished());
+	
+	// Set up transmitter
+	Real momtemp;
+	momtemp = 1;
+	Real freq;
+	freq = 391;
+	Trans->SetType(MAGNETICDIPOLE);
+	Trans->SetLocation(0,0,-1.e-3);
+	Trans->SetPolarisation(ZPOLARISATION);
+	// as a test
+	Trans->SetNumberOfFrequencies(1);
+	Trans->SetFrequency(0,freq);
+	Trans->SetMoment(momtemp);
+
+	// Set up receivers
+	Vector3r loc1;
+	Vector3r loc2;
+	Receivers->SetNumberOfReceivers(1);
+	loc1 << 9,0,-1.e-3;
+	Receivers->SetLocation(0,loc1);
+
+
+	// Attach to instrument
+	theinstrument->SetReceiverPoints(Receivers);
+	theinstrument->SetDipoleSource(Trans);
+	theinstrument->EMEarthModel(Earth);
+	theinstrument->SetOutputData(modelledData);
+
+	// Calculate
+	theinstrument->MakeCalculation();
+
+	// See what comes back...
+	std::cout << Receivers->GetHfield(0,0)(2) << std::endl;
+	
+	// Need to convert H field to ppm
+
+
+	theinstrument->Delete();
+	modelledData->Delete();
+
+	// MULTIPLE SOUNDING MODEL USING READ-IN DATA
+
+
+	InstrumentFem* theinstrument2 = InstrumentFem::New();
+	DataFEM* modelledData2 = DataFEM::New();
+
+	// Using the UBC data reader to read in the survey params
+	// this will be used for the multiple sounding testing
+	std::string datfile;
+	datfile = "126.obs";
+
+	DataReaderFemUBC* Reader = DataReaderFemUBC::New();
+	DataFEM* inpdata = DataFEM::New();
+	Reader->SetDataFEM(inpdata);
+	try {
+		Reader->ReadData(datfile,1);
+	} catch(std::exception& e) {
+		exit(EXIT_FAILURE);
+	}
+	std::cout << *inpdata << std::endl;
+	theinstrument2->SetOutputData(modelledData2);
+	theinstrument2->AlignWithData(inpdata);
+	// Now, how do I want to pass it an earth model for each sounding?
+	//
+	inpdata->Delete();
+
+
+
+
+	// Need to loop over transmitters
+	// The relative positions of the transmitter and receiver is fixed
+	// For testing, do some kind of random realisation of Earth model?
+//	int nObs;
+//	int nFreqs;
+//	nObs = inpdata->GetnObs();
+//	nFreqs = inpdata->GetnFreq();
+
+//	Trans->SetType(MAGNETICDIPOLE);
+//	Trans->SetLocation(0,0,-1e-3);
+
+//	Vector3r loc;
+//	Receivers->SetNumberOfReceivers(1);
+//	loc << 0,0,-1e-3;
+//	Receivers->SetLocation(0,loc);
+
+//	Earth->SetNumberOfLayers(5); //Including the two halfspaces
+//	Earth->SetLayerConductivity((VectorXcr(5) << 0.,1.e-4,1.e-2,
+//		1.e-4,1.e-6).finished());
+//	Earth->SetLayerThickness((VectorXr(3) << 20.,5.,50.).finished());
+
+//	for (int ii=0;ii<nObs;ii++) {
+//		for (int jj=0;jj<nFreqs;jj++) {
+//			Trans->SetMoment(inpdata->GetTxMom().coeff(jj));
+//			
+//		}
+//	}
+	
+	//This is a bunch of testing stuff
+	//theinstrument->AlignWithData(inpdata);
+	//theinstrument->MakeCalculation();
+	//inpdata->Delete();
+	//theinstrument->MakeCalculation();
+
+
+	theinstrument2->Delete();
+	Reader->Delete();
+	Earth->Delete();
+	Receivers->Delete();
+	Trans->Delete();
+
+	// Timey-wimey stuff
+	Real time;
+	clock_t done = clock();
+	time = (done-launch)/CLOCKS_PER_SEC;
+	std::cout << "  Execution time: " << time << " [CPU] seconds."
+		<< std::endl;
+
+	return EXIT_SUCCESS;
+}

Modules/FDEM1D/src/gaussianquadrature.cpp

@@ -0,0 +1,138 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   M. Andy Kass
+  @date     10/07/2010
+  @version  $Id: gaussianquadrature.cpp 87 2013-09-05 22:44:05Z tirons $
+ **/
+
+#include "gaussianquadrature.h"
+
+namespace Lemma {
+
+//	std::ostream &operator<<(std::ostream &stream,
+//				const gaussianquadrature &ob) {
+//
+//	}
+
+	////////////////////////////////////////////////
+	gaussianquadrature::gaussianquadrature() {
+	}
+	gaussianquadrature::~gaussianquadrature() {
+	}
+	gaussianquadrature* gaussianquadrature::New() {
+		return new gaussianquadrature;
+	}
+	void gaussianquadrature::Delete() {
+		delete this;
+	}
+
+	////////////////////////////////////////////////
+	void gaussianquadrature::Integrate() {
+
+		this->intres=(this->funcx.array()*this->wgq.array()).sum();
+
+	}
+
+	////////////////////////////////////////////////
+	void gaussianquadrature::CalcAW() {
+
+		while ((this->y-this->y0).array().abs().maxCoeff()>
+				this->machineeps) {
+			this->L.col(0).setOnes();
+			this->Ltemp.col(0).setZero();
+			this->L.col(1)=this->y;
+			this->Ltemp.col(1).setOnes();
+
+			for (int kk=2;kk<this->N2;++kk) {
+				this->ytemp=this->L.col(kk-1).array()*this->y.array();
+				this->ytemp=this->ytemp.array()*(2.0*Real(kk)-1.0);
+				this->L.col(kk)=this->ytemp.array()-((Real(kk)-1.0)*
+					this->L.col(kk-2).array());
+				this->L.col(kk)=this->L.col(kk).array()/Real(kk);
+			}
+			this->ytemp=this->y.array()*this->L.col(this->N1).array();
+			this->Lp=this->L.col(this->N1-1)-this->ytemp;
+			this->Lp=this->Lp.array()/(1.0-(this->y.array()*this->y.array()));
+			this->Lp=this->Lp.array()*this->N2;
+			this->y0=this->y;
+			this->ytemp=this->L.col(this->N1);
+			this->y=this->y0.array()-(this->ytemp.array()/this->Lp.array());
+		}
+
+		for (int ii=0;ii<this->N1;++ii) {
+			this->xu(ii)=((this->b-this->a)*((this->y(ii)+1.0)/2.0))+this->a;
+			this->wgq(ii)=((this->b-this->a)/((1.0-(this->y(ii)*this->y(ii)))*
+				(this->Lp(ii)*this->Lp(ii))))*((Real(this->N2)/Real(this->N1))*
+				(Real(this->N2)/Real(this->N1)));
+		}
+	}
+
+	////////////////////////////////////////////////
+	void gaussianquadrature::SetFreqs(const int& nfreq,
+			const Real& a, const Real& b) {
+		this->N = nfreq-1;
+		this->N1 = nfreq;
+		this->N2 = nfreq+1;
+		// \TODO Use pointers here instead
+		this->a = a;
+		this->b = b;
+
+		//Debugging only
+		//std::cout << N << "   " << a << "   " << b << std::endl;
+
+		this->dx = (2.0)/Real(nfreq);
+		this->machineeps = std::numeric_limits<Real>::epsilon();
+
+		this->ytemp.resize(this->N1);
+		this->xu.resize(this->N1);
+		this->y.resize(this->N1);
+		this->y0.resize(this->N1);
+		this->Lp.resize(this->N1);
+		this->wgq.resize(this->N1);
+		// \TODO Instead of copying the variable, use pointers
+		this->funcx.resize(nfreq);
+
+		this->L.resize(this->N1,this->N2);
+		this->Ltemp.resize(this->N1,this->N2);
+
+		for (int ii=0;ii<this->N1;++ii) {
+			this->xu(ii)=(dx*Real(ii))-1.0;
+			this->y(ii)=std::cos((2.0*Real(ii)+1.0)*PI/(2.0*
+				Real(this->N)+2.0))+(0.27/(Real(this->N1)))*
+				std::sin(PI*xu(ii)*Real(this->N)/(Real(this->N2)));
+			this->y0(ii)=2.0;
+			this->ytemp(ii)=0.0;
+		}
+	}
+
+	////////////////////////////////////////////////
+	void gaussianquadrature::SetFunc(const VectorXr& fx) {
+		this->funcx = fx;
+	}
+
+	////////////////////////////////////////////////
+	VectorXr gaussianquadrature::GetAbscissae() {
+
+		return this->xu;
+	}
+
+	////////////////////////////////////////////////
+	VectorXr gaussianquadrature::GetWeights() {
+
+		return this->wgq;
+	}
+
+	////////////////////////////////////////////////
+	Real gaussianquadrature::GetResult() {
+
+		return intres;
+	}
+
+} //end of namespace Lemma
+

Modules/FDEM1D/src/hankeltransform.cpp

@@ -0,0 +1,39 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     01/02/2010
+  @version  $Id: hankeltransform.cpp 193 2014-11-10 23:51:41Z tirons $
+ **/
+
+#include "hankeltransform.h"
+
+namespace Lemma {
+
+	std::ostream &operator<<(std::ostream &stream,
+			const HankelTransform &ob) {
+		stream << *(LemmaObject*)(&ob);
+		return stream;
+	}
+
+	HankelTransform::HankelTransform(const std::string &name) :
+	   LemmaObject(name)	{
+	}
+
+	HankelTransform::~HankelTransform() {
+	}
+
+    void HankelTransform::ComputeRelated(const Real& rho, KernelEm1DBase *Kernel) {
+    }
+
+    void HankelTransform::ComputeRelated(const Real& rho, std::vector< KernelEm1DBase* > KernelVec) {
+    }
+
+    void HankelTransform::ComputeRelated(const Real& rho, KernelEM1DManager*  KernelManager) {
+    }
+}

Modules/FDEM1D/src/instrumentfem.cpp

@@ -0,0 +1,174 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   M. Andy Kass
+  @date     01/14/2013
+  @version  $Id$
+ **/
+
+#include "instrumentfem.h"
+
+namespace Lemma {
+
+	std::ostream &operator<<(std::ostream &stream,
+		const InstrumentFem &ob) {
+		stream << *(LemmaObject*)(&ob);
+		return stream;
+	}
+
+	InstrumentFem::InstrumentFem(const std::string &name) : Instrument (name),
+		EarthModel(NULL), Dipole(NULL), Receiver(NULL), InputData(NULL),
+	    OutputData(NULL)	{
+		}
+
+	InstrumentFem::~InstrumentFem() {
+		if (NumberOfReferences !=0) {
+			throw DeleteObjectWithReferences(this);
+		}
+	}
+
+	InstrumentFem* InstrumentFem::New() {
+		InstrumentFem* Obj = new InstrumentFem("InstrumentFem");
+		Obj->AttachTo(Obj);
+		return Obj;
+	}
+
+	void InstrumentFem::Delete() {
+		this->DetachFrom(this);
+	}
+
+	void InstrumentFem::Release() {
+		delete this;
+	}
+
+	void InstrumentFem::MakeCalculation() {
+
+		EMEarth1D *EMEarthLocal=EMEarth1D::New();
+		EMEarthLocal->AttachLayeredEarthEM(this->EarthModel);
+		EMEarthLocal->AttachDipoleSource(this->Dipole);
+		EMEarthLocal->SetFieldsToCalculate(H);
+		//EMEarthLocal->SetHankelTransformMethod(DIGITALFILTERING);
+		EMEarthLocal->SetHankelTransformMethod(CHAVE);
+		EMEarthLocal->AttachReceiverPoints(this->Receiver);
+		EMEarthLocal->MakeCalc3();
+		//EMEarthLocal->MakeCalc();
+
+		EMEarthLocal->Delete();
+
+		// GetHfield(freq_idx, loc_idx)(comp)
+
+	}
+
+	void InstrumentFem::ForwardModelProfile() {
+
+
+	}
+
+	void InstrumentFem::EMEarthModel(LayeredEarthEM* Earth) {
+		if (this->EarthModel != NULL) {
+			this->EarthModel->DetachFrom(this);
+		}
+		Earth->AttachTo(this);
+		this->EarthModel = Earth;
+	}
+
+	void InstrumentFem::SetDipoleSource(DipoleSource* dipolesource) {
+		if (this->Dipole != NULL) {
+			this->Dipole->DetachFrom(this);
+		}
+		dipolesource->AttachTo(this);
+		this->Dipole = dipolesource;
+	}
+
+	void InstrumentFem::SetReceiverPoints(ReceiverPoints* receiver) {
+		if (this->Receiver != NULL) {
+			this->Receiver->DetachFrom(this);
+		}
+		receiver->AttachTo(this);
+		this->Receiver = receiver;
+	}
+
+	void InstrumentFem::AlignWithData(DataFEM* inpdata) {
+		this->nFreq = inpdata->GetnFreq();
+		this->nObs = inpdata->GetnObs();
+		this->freq = inpdata->GetFreqs();
+		this->xyz = inpdata->GetXYZ();
+		this->TxOrientation = inpdata->GetTxOrien();
+		this->RxOrientation = inpdata->GetRxOrien();
+		this->TxMom = inpdata->GetTxMom();
+		this->TxRxSep = inpdata->GetTxRxSep();
+		this->ScaleFac = inpdata->GetScaleFac();
+
+		// Check into boost for the use of pointer arrays
+		// array of nFreq DipoleSource objects
+			//first get rid of existing dipoles
+		for (unsigned int id=0;id<this->Transmitters.size();++id) {
+			this->Transmitters[id]->Delete();
+		}
+		this->Transmitters.clear();
+		//this->Transmitters.resize(this->nFreq);
+
+		for (unsigned int id=0;id<this->Receivers.size();++id) {
+			this->Receivers[id]->Delete();
+		}
+		this->Receivers.clear();
+
+
+		for (int ii=0;ii<this->nFreq;ii++) {
+			/*
+			this->Transmitters.push_back(DipoleSource::New());
+			std::cout << &(this->Transmitters[ii]) << std::endl;
+			*/
+			DipoleSource *tt = DipoleSource::New();
+			ReceiverPoints *tr = ReceiverPoints::New();
+			Real ftemp;
+			Real momtemp;
+			ftemp = this->freq(ii);
+			momtemp = this->TxMom(ii);
+			tt->SetType(MAGNETICDIPOLE);
+			tt->SetLocation(0,0,-1.e-3);
+			// This is really hoopty but will do for now
+			if (this->TxOrientation(ii) == X) {
+				tt->SetPolarisation(XPOLARISATION);
+			}
+			else if (this->TxOrientation(ii) == Y) {
+				tt->SetPolarisation(YPOLARISATION);
+			}
+			else if (this->TxOrientation(ii) == Z) {
+				tt->SetPolarisation(ZPOLARISATION);
+			}
+			else {
+				std::cout << "DANGER! DANGER! UNHELPFUL ERROR"
+					 << std::endl;
+				tt->SetPolarisation(ZPOLARISATION);
+			}
+			tt->SetNumberOfFrequencies(1);
+			tt->SetFrequency(0,ftemp);
+			tt->SetMoment(momtemp);
+			this->Transmitters.push_back(tt);
+			tr->SetNumberOfReceivers(1);
+			tr->SetLocation(0,this->TxRxSep.block(0,ii,3,1));
+			this->Receivers.push_back(tr);
+		}
+
+		// Now populate the attached output data object?
+		// Or, should I do this later after the computation?
+
+	}
+
+	void InstrumentFem::SetOutputData(DataFEM* outputdata) {
+		if (this->OutputData != NULL) {
+			this->OutputData->DetachFrom(this);
+		}
+		outputdata->AttachTo(this);
+		this->OutputData = outputdata;
+	}
+
+
+
+}// end of namespace lemma

Modules/FDEM1D/src/integrationkernel.cpp

@@ -0,0 +1,27 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     02/07/2011
+  @version  $Id: integrationkernel.cpp 193 2014-11-10 23:51:41Z tirons $
+ **/
+
+#include "integrationkernel.h"
+
+namespace Lemma {
+
+    template <typename T>
+    IntegrationKernel<T>::IntegrationKernel(const std::string& name) :
+        LemmaObject(name) {
+    }
+
+    template<typename T>
+    IntegrationKernel<T>::~IntegrationKernel( ) {
+    }
+
+}		// -----  end of Lemma  name  -----

Modules/FDEM1D/src/inversesolver.cpp

@@ -0,0 +1,78 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     07/14/2010
+  @version  $Id: inversesolver.cpp 193 2014-11-10 23:51:41Z tirons $
+ **/
+
+#include "inversesolver.h"
+
+namespace Lemma {
+
+    std::ostream &operator<<(std::ostream &stream,
+                const InverseSolver &ob) {
+        stream << *(LemmaObject*)(&ob);
+        return stream;
+    }
+
+    // ====================  LIFECYCLE     =======================
+
+    InverseSolver::InverseSolver(const std::string &name) :
+        LemmaObject(name), ObservedData(NULL),
+        PredictedData(NULL), ModelInstrument(NULL) {
+    }
+
+    InverseSolver::~InverseSolver() {
+
+        if (NumberOfReferences != 0) throw DeleteObjectWithReferences(this);
+
+        if (ObservedData != NULL)    ObservedData->DetachFrom(this);
+
+        if (PredictedData != NULL) {
+            PredictedData->Delete();
+        }
+
+        if (ModelInstrument != NULL)       ModelInstrument->DetachFrom(this);
+    }
+
+    // ====================  ACCESS        =======================
+
+    void InverseSolver::SetObservedData(Data* ObsData) {
+
+        if (ObservedData != NULL) {
+            ObservedData->DetachFrom(this);
+            ObservedData = NULL;
+        }
+
+        if (PredictedData != NULL) {
+            PredictedData->Delete();
+            PredictedData = NULL;
+        }
+
+        ObsData->AttachTo(this);
+        this->ObservedData = ObsData;
+
+        // Obs and predicted data need to be aligned.
+        PredictedData = ObservedData->Clone();
+        //PredictedData->AttachTo(this);
+    }
+
+    void InverseSolver::SetInstrument(Instrument* inst) {
+        if (ModelInstrument != NULL) {
+            ModelInstrument->DetachFrom(this);
+        }
+        inst->AttachTo(this);
+        this->ModelInstrument = inst;
+    }
+
+    Data* InverseSolver::GetPredictedData() {
+        return PredictedData; //->ThrowPointer();
+    }
+
+}		// -----  end of Lemma  name  -----

Modules/FDEM1D/src/kernel.cpp

@@ -0,0 +1,29 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     01/29/2010
+  @version  $Id: kernel.cpp 193 2014-11-10 23:51:41Z tirons $
+ **/
+
+#include "kernel.h"
+namespace Lemma {
+
+	std::ostream &operator<<(std::ostream &stream,
+				const Kernel &ob) {
+		stream << *(LemmaObject*)(&ob);
+		return stream;
+	}
+
+	Kernel::Kernel(const std::string& name) :
+			LemmaObject(name) {
+	}
+
+	Kernel::~Kernel() {
+	}
+}

Modules/FDEM1D/src/kernelem1dmanager.cpp

@@ -0,0 +1,128 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     06/26/2012
+  @version  $Id: kernelem1dmanager.cpp 193 2014-11-10 23:51:41Z tirons $
+ **/
+
+#include "kernelem1dmanager.h"
+
+
+namespace Lemma {
+
+    std::ostream &operator<<(std::ostream &stream,
+                const KernelEM1DManager &ob) {
+        stream << *(LemmaObject*)(&ob);
+        return stream;
+    }
+
+
+    // ====================  LIFECYCLE     =======================
+
+    KernelEM1DManager::KernelEM1DManager(const std::string& name) :
+                    LemmaObject(name), TEReflBase(NULL), TMReflBase(NULL), Earth(NULL), Dipole(NULL) {
+    }
+
+    KernelEM1DManager::~KernelEM1DManager() {
+
+        if (this->NumberOfReferences != 0)
+            throw DeleteObjectWithReferences(this);
+
+//         if (Earth != NULL) {
+//             Earth->DetachFrom(this);
+//         }
+//
+//         if (Dipole != NULL) {
+//             Dipole->DetachFrom(this);
+//         }
+
+        for (unsigned int ik=0; ik<KernelVec.size(); ++ik) {
+            KernelVec[ik]->Delete();
+        }
+
+        if (TEReflBase != NULL) TEReflBase->Delete();
+        if (TMReflBase != NULL) TMReflBase->Delete();
+
+    }
+
+    KernelEM1DManager* KernelEM1DManager::New() {
+        KernelEM1DManager* Obj = new KernelEM1DManager("KernelEM1DManager");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    void KernelEM1DManager::Delete() {
+        this->DetachFrom(this);
+    }
+
+    void KernelEM1DManager::Release() {
+        delete this;
+    }
+
+    // ====================  ACCESS        =======================
+
+    // A race condition can develop with these. It's OK to not attach, since this is an internal class, and
+    // we know what is going on.
+    void KernelEM1DManager::SetEarth(LayeredEarthEM* Earthin) {
+        //if (Earth != NULL) {
+        //    Earth->DetachFrom(this);
+        //}
+        //Earthin->AttachTo(this);
+        Earth = Earthin;
+    }
+
+    void KernelEM1DManager::SetDipoleSource(DipoleSource* DipoleIn, const int& ifreqin,
+            const Real& rx_zin) {
+        //if (Dipole != NULL) {
+        //    Dipole->DetachFrom(this);
+        //}
+        //DipoleIn->AttachTo(this);
+        Dipole = DipoleIn;
+
+        ifreq = ifreqin;
+        rx_z = rx_zin;
+    }
+
+    KernelEm1DBase* KernelEM1DManager::GetKernel(const unsigned int& ik) {
+        return KernelVec[ik];
+    }
+
+    DipoleSource* KernelEM1DManager::GetDipole( ) {
+        return Dipole;
+    }
+
+    // ====================  OPERATIONS    =======================
+
+    void KernelEM1DManager::ComputeReflectionCoeffs(const Real& lambda, const int& idx, const Real& rho0) {
+
+        if (TEReflBase != NULL) {
+            TEReflBase->ComputeReflectionCoeffs(lambda);
+            TEReflBase->PreComputePotentialTerms( );
+        }
+
+        if (TMReflBase != NULL) {
+            TMReflBase->ComputeReflectionCoeffs(lambda);
+            TMReflBase->PreComputePotentialTerms( );
+        }
+
+    }
+
+    void KernelEM1DManager::ResetSource(const int& ifreq) {
+
+        if (TEReflBase != NULL) {
+            TEReflBase->SetUpSource(Dipole, ifreq);
+        }
+
+        if (TMReflBase != NULL) {
+            TMReflBase->SetUpSource(Dipole, ifreq);
+
+        }
+    }
+
+}		// -----  end of Lemma  name  -----

Modules/FDEM1D/src/kernelem1dreflspec.cpp

@@ -0,0 +1,241 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     05/18/2012
+  @version  $Id: kernelem1dreflspec.cpp 169 2014-09-06 22:16:12Z tirons $
+ **/
+
+#include "kernelem1dreflspec.h"
+
+namespace Lemma {
+
+    template<>
+    void KernelEM1DReflSpec<TM, INAIR, INAIR>::ComputeReflectionCoeffs(const Real& lambda) {
+
+        rams = lambda*lambda;
+        u = (rams-kk.array()).sqrt(); // CRITICAL
+        uk = u(0);
+        um = u(0);
+
+        Zyu(1) = -u(0)/yh(0);
+        Zyi    =  u.array() / yh.array();
+
+        Zyd.tail<1>() = Zyi.tail<1>();
+
+        // Vectorise, performance is not really any better
+        cf.segment(1,nlay-2) = (-2.*u.segment(1, nlay-2).array() * LayerThickness.segment(1, nlay-2).array()).exp();
+        th.segment(1,nlay-2) = (1.-cf.segment(1, nlay-2).array()) / (1.+cf.segment(1, nlay-2).array());
+
+        /*
+        for (int ilay=1; ilay<nlay-1; ++ilay) {
+            cf(ilay) = std::exp(-(Real)(2.)*u(ilay)*LayerThickness(ilay));
+            th(ilay) = ((Real)(1.)-cf(ilay)) / ((Real)(1.)+cf(ilay));
+        }
+        */
+
+        // recursive, can't vectorize
+        for (int N=nlay-2; N >= 1; --N) {
+            Zyd(N) = Zyi(N)*(Zyd(N+1)+Zyi(N)*th(N)) / (Zyi(N)+Zyd(N+1)*th(N)) ;
+        }
+
+        //rtd(nlay-1) = 0;
+        rtd(0) = (Zyu(1)+Zyd(1)) / (Zyu(1)-Zyd(1)) ;
+
+        return;
+    }
+
+    template<>
+    void KernelEM1DReflSpec<TE, INAIR, INAIR>::ComputeReflectionCoeffs(const Real& lambda) {
+
+        rams = lambda*lambda;
+        u = (rams-kk.array()).sqrt(); // CRITICAL
+        uk = u(0);
+        um = u(0);
+
+        Zyu(1) = -u(0)/zh(0);
+        Zyi    =  u.array() / zh.array();
+
+        Zyd.tail<1>() = Zyi.tail<1>();
+
+        // Vectorise
+        cf.segment(1,nlay-2) = (-2.*u.segment(1, nlay-2).array() * LayerThickness.segment(1, nlay-2).array()).exp();
+        th.segment(1,nlay-2) = (1.-cf.segment(1, nlay-2).array()) / (1.+cf.segment(1, nlay-2).array());
+
+        /*
+        for (int ilay=1; ilay<nlay-1; ++ilay) {
+            cf(ilay) = std::exp(-(Real)(2.)*u(ilay)*LayerThickness(ilay));
+            th(ilay) = ((Real)(1.)-cf(ilay)) / ((Real)(1.)+cf(ilay));
+        }
+        */
+
+        // recursive, can't vectorize
+        for (int N=nlay-2; N >=1; --N) {
+            Zyd(N) = Zyi(N)*(Zyd(N+1)+Zyi(N)*th(N)) / (Zyi(N)+Zyd(N+1)*th(N)) ;
+        }
+
+        //rtd(nlay-1) = 0;
+        rtd(0) = (Zyu(1)+Zyd(1)) / (Zyu(1)-Zyd(1)) ;
+
+        return;
+    }
+
+    template<>
+    void KernelEM1DReflSpec<TM, INAIR, INGROUND>::ComputeReflectionCoeffs(const Real& lambda) {
+
+        rams = lambda*lambda;
+        u = (rams-kk.array()).sqrt();
+        uk = u(0);
+        um = u(layr);
+
+        Zyu(1) = -u(0)/yh(0);
+        Zyi    =  u.array() / yh.array();
+
+        Zyd.tail<1>() = Zyi.tail<1>();
+
+        for (int ilay=1; ilay<nlay-1; ++ilay) {
+            cf(ilay) = std::exp(-(Real)(2.)*u(ilay)*LayerThickness(ilay));
+            th(ilay) = ((Real)(1.)-cf(ilay)) / ((Real)(1.)+cf(ilay));
+        }
+
+        // Can't use blocks, b/c recursive
+        for (int N=1; N<lays; ++N){
+            Zyu(N+1)=Zyi(N)*(Zyu(N)-Zyi(N)*th(N)) /
+                            (Zyi(N)-Zyu(N)*th(N)) ;
+        }
+
+        int ne = nlay-2;
+        for (int N=ne; N >=lays+1; --N) {
+            Zyd(N) = Zyi(N)*(Zyd(N+1)+Zyi(N)*th(N)) /
+                            (Zyi(N)+Zyd(N+1)*th(N)) ;
+        }
+
+        rtd(nlay-1) = 0;
+        rtd(0) = (Zyu(1)+Zyd(1)) / (Zyu(1)-Zyd(1)) ;
+
+        int le = layr;
+        if (le == nlay-1) --le;
+        for (int N=1; N<=le; ++N) {
+            rtd(N) = (Zyi(N)-Zyd(N+1)) / (Zyi(N)+Zyd(N+1)) ;
+        }
+        return;
+    }
+
+    template<>
+    void KernelEM1DReflSpec<TE, INAIR, INGROUND>::ComputeReflectionCoeffs(const Real& lambda) {
+
+        rams = lambda*lambda;
+        u = (rams-kk.array()).sqrt();
+        uk = u(0);
+        um = u(layr);
+
+        Zyu(1) = -u(0)/zh(0);
+        Zyi    =  u.array() / zh.array();
+
+        Zyd.tail<1>() = Zyi.tail<1>();
+
+        for (int ilay=1; ilay<nlay-1; ++ilay) {
+            cf(ilay) = std::exp(-(Real)(2.)*u(ilay)*LayerThickness(ilay));
+            th(ilay) = ((Real)(1.)-cf(ilay)) / ((Real)(1.)+cf(ilay));
+        }
+
+        // Can't use blocks, b/c recursive
+        for (int N=1; N<lays; ++N){
+            Zyu(N+1)=Zyi(N)*(Zyu(N)-Zyi(N)*th(N)) /
+                            (Zyi(N)-Zyu(N)*th(N)) ;
+        }
+
+        int ne = nlay-2;
+        for (int N=ne; N >=lays+1; --N) {
+            Zyd(N) = Zyi(N)*(Zyd(N+1)+Zyi(N)*th(N)) /
+                            (Zyi(N)+Zyd(N+1)*th(N)) ;
+        }
+
+        rtd(nlay-1) = 0;
+        rtd(0) = (Zyu(1)+Zyd(1)) / (Zyu(1)-Zyd(1)) ;
+
+        int le = layr;
+        if (le == nlay-1) --le;
+        for (int N=1; N<=le; ++N) {
+            rtd(N) = (Zyi(N)-Zyd(N+1)) / (Zyi(N)+Zyd(N+1)) ;
+        }
+        return;
+    }
+
+    template<>
+    void KernelEM1DReflSpec<TM, INAIR, INAIR>::PreComputePotentialTerms( ) {
+        relIud = 0;
+        if (rx_z<= tx_z) relIud=1;
+        relCon = rtd(0)*std::exp(u(0)*(rx_z+tx_z));
+        Real adz = std::abs(rx_z - tx_z);
+        relenukadz = std::exp(-uk*adz); // Singular source term
+    }
+
+    template<>
+    void KernelEM1DReflSpec<TE, INAIR, INAIR>::PreComputePotentialTerms( ) {
+        relIud = 0;
+        if (rx_z<= tx_z) relIud=1;
+        relCon = rtd(0)*std::exp(u(0)*(rx_z+tx_z));
+        Real adz = std::abs(rx_z - tx_z);
+        relenukadz = std::exp(-uk*adz); // Singular source term
+    }
+
+    template<>
+    void KernelEM1DReflSpec<TM, INAIR, INGROUND>::PreComputePotentialTerms( ) {
+        Complex dd =  ((Real)(1.)+rtd(1)*cf(1));
+        rel_a = ((Real)(1.) + rtd(0)) / dd;
+        if (layr >= 2) {
+            for (int n=2; n<=layr; ++n) {
+                rel_a *= ((Real)(1.)+rtd(n-1));
+                if (n < nlay-1) {
+                    rel_a /= ((Real)(1.)+rtd(n)*cf(n));
+                }
+            }
+        }
+        Complex p(0,0);
+        for (int n=1; n<=layr; ++n) {
+            Complex ut = u(0);
+            if (n>1) {
+                ut = u(n-1);
+            }
+            p += (u(n)-ut) * LayerDepth(n-1);
+        }
+        relexp_pbs1 = std::exp(uk*tx_z-um*rx_z+ p);
+
+        if (layr < Earth->GetNumberOfLayers()-1) {
+            relexp_pbs2 = std::exp(uk*tx_z-um*((Real)(2.)*LayerDepth(layr)-rx_z)+p);
+        }
+    }
+
+    template<>
+    void KernelEM1DReflSpec<TE, INAIR, INGROUND>::PreComputePotentialTerms( ) {
+        Complex dd =  ((Real)(1.)+rtd(1)*cf(1));
+        rel_a = ((Real)(1.) + rtd(0)) / dd;
+        if (layr >= 2) {
+            for (int n=2; n<=layr; ++n) {
+                rel_a *= ((Real)(1.)+rtd(n-1));
+                if (n < nlay-1) {
+                    rel_a /= ((Real)(1.)+rtd(n)*cf(n));
+                }
+            }
+        }
+        Complex p(0,0);
+        for (int n=1; n<=layr; ++n) {
+            Complex ut = u(0);
+            if (n>1) {
+                ut = u(n-1);
+            }
+            p += (u(n)-ut) * LayerDepth(n-1);
+        }
+        relexp_pbs1 = std::exp(uk*tx_z-um*rx_z+ p);
+        if (layr < Earth->GetNumberOfLayers()-1) {
+            relexp_pbs2 = std::exp(uk*tx_z-um*((Real)(2.)*LayerDepth(layr)-rx_z)+p);
+        }
+    }
+
+}		// -----  end of Lemma  name  -----

Modules/FDEM1D/src/layeredearthem.cpp

@@ -0,0 +1,361 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     06/24/2009
+  @version  $Id: layeredearthem.cpp 216 2015-03-09 02:26:49Z tirons $
+ **/
+
+#include "layeredearthem.h"
+
+namespace Lemma {
+
+#ifdef HAVE_YAMLCPP
+    std::ostream &operator << (std::ostream &stream, const LayeredEarthEM &ob) {
+        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
+        return stream;
+    }
+#else
+    std::ostream &operator<<(std::ostream &stream,
+                const LayeredEarthEM &ob) {
+        stream << *(LayeredEarth*)(&ob);
+        //stream << "Class Name : "<< ob.Name  << "\n";
+        stream << std::setw(15) << "LayerNumber"         << "\t"
+               << std::setw(15) << "Thickness"           << "\t"
+               << std::setw(15) << "BottomInterface"     << "\t"
+               << std::setw(15) << "Conductivity"        << "\t"
+               << std::setw(15) << "Susceptibility"      << "\t"
+               << std::setw(15) << "Permitivity"         << "\n";
+        stream << std::setw(15) << " "                   << "\t"
+               << std::setw(15) << "[m]"                 << "\t"
+               << std::setw(15) << "[m]"                 << "\t"
+               << std::setw(15) << "[Sm^-1]"             << "\t"
+               << std::setw(15) << "[]"                  << "\t"
+               << std::setw(15) << "[F/m]"               << "\n";
+        for (int i=0; i< ob.NumberOfLayers; ++i) {
+            stream << std::setw(15) <<  i << "\t"
+                   << std::setw(15) << ((LayeredEarth*)(&ob))->GetLayerThickness(i) << "\t"
+                   << std::setw(15) << ((LayeredEarth*)(&ob))->GetLayerDepth(i) << "\t"
+                   << std::setw(15) << ob.LayerConductivity(i)     << "\t"
+                   << std::setw(15) << ob.LayerSusceptibility(i)   << "\t"
+                   << std::setw(15) << ob.LayerPermitivity(i)      << "\n";
+        }
+
+        return stream;
+    }
+#endif
+
+    // ====================  LIFECYCLE     ===================================
+
+    LayeredEarthEM::LayeredEarthEM(const std::string &name) :
+        LayeredEarth(name) {
+    }
+
+    LayeredEarthEM::~LayeredEarthEM() {
+        if (NumberOfReferences != 0) {
+            throw DeleteObjectWithReferences(this);
+        }
+    }
+
+    LayeredEarthEM* LayeredEarthEM::New() {
+        LayeredEarthEM* Obj = new LayeredEarthEM("LayeredEarthEM");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    void LayeredEarthEM::Delete() {
+        this->DetachFrom(this);
+    }
+
+    void LayeredEarthEM::Release() {
+        delete this;
+    }
+
+    #ifdef HAVE_YAMLCPP
+    YAML::Node LayeredEarthEM::Serialize() const {
+        YAML::Node node = LayeredEarth::Serialize();
+        node.SetTag( this->Name );
+        node["LayerConductivity"] = LayerConductivity;
+        node["LayerSusceptibility"] = LayerSusceptibility;
+        node["LayerLowFreqSusceptibility"] = LayerLowFreqSusceptibility;
+        node["LayerHighFreqSusceptibility"] = LayerHighFreqSusceptibility;
+        node["LayerTauSusceptibility"] = LayerTauSusceptibility;
+        node["LayerBreathSusceptibility"] = LayerBreathSusceptibility;
+        node["LayerPermitivity"] = LayerPermitivity;
+        node["LayerLowFreqPermitivity"] = LayerLowFreqPermitivity;
+        node["LayerHighFreqPermitivity"] = LayerHighFreqPermitivity;
+        node["LayerTauPermitivity"] = LayerTauPermitivity;
+        node["LayerBreathPermitivity"] = LayerBreathPermitivity;
+        return node;
+    }
+    #endif
+
+    // ====================  OPERATIONS    ===================================
+    void LayeredEarthEM::EvaluateColeColeModel(const Real& omega) {
+
+        for (int ilay=0; ilay<NumberOfLayers; ++ilay) {
+            if ( LayerTauSusceptibility(ilay) > 1e-10) {
+                LayerSusceptibility(ilay) = LayerHighFreqSusceptibility(ilay) + (LayerLowFreqSusceptibility(ilay) -
+                     LayerHighFreqSusceptibility(ilay)) /
+                    ((Real)(1.) + std::pow(Complex(0, omega*
+                                    LayerTauSusceptibility(ilay)),
+                             LayerBreathSusceptibility(ilay)));
+            } else {
+                LayerSusceptibility(ilay) = LayerLowFreqSusceptibility(ilay);
+            }
+
+            if ( LayerTauPermitivity(ilay) > 1e-10) {
+                LayerPermitivity(ilay) = LayerHighFreqPermitivity(ilay) +
+                    (LayerLowFreqPermitivity(ilay) -
+                     LayerHighFreqPermitivity(ilay)) /
+                    ((Real)(1.) + std::pow(Complex(0,
+                                    omega*LayerTauPermitivity(ilay)),
+                            LayerBreathPermitivity(ilay)));
+            } else {
+                LayerPermitivity(ilay) = LayerLowFreqPermitivity(ilay);
+            }
+        }
+    }
+
+	LayeredEarthEM* LayeredEarthEM::Clone() {
+		LayeredEarthEM* copy = LayeredEarthEM::New();
+
+		copy->LayerConductivity = this->LayerConductivity;
+		copy->LayerSusceptibility = this->LayerSusceptibility;
+		copy->LayerLowFreqSusceptibility = this->LayerLowFreqSusceptibility;
+		copy->LayerHighFreqSusceptibility = this->LayerHighFreqSusceptibility;
+		copy->LayerTauSusceptibility = this->LayerTauSusceptibility;
+		copy->LayerBreathSusceptibility = this->LayerBreathSusceptibility;
+		copy->LayerPermitivity = this->LayerPermitivity;
+		copy->LayerLowFreqPermitivity = this->LayerLowFreqPermitivity;
+		copy->LayerHighFreqPermitivity = this->LayerHighFreqPermitivity;
+		copy->LayerTauPermitivity = this->LayerTauPermitivity;
+		copy->LayerBreathPermitivity = this->LayerBreathPermitivity;
+		copy->NumberOfLayers = this->NumberOfLayers;
+		copy->NumberOfInterfaces = this->NumberOfInterfaces;
+		copy->LayerThickness = this->LayerThickness;
+
+		return copy;
+
+	}
+
+    // ====================  ACCESS        ==================================
+
+    void LayeredEarthEM::SetLayerConductivity(const VectorXcr &sig) {
+        if (sig.size() != this->NumberOfLayers )
+            throw EarthModelParametersDoNotMatchNumberOfLayers( );
+        LayerConductivity = sig;
+    }
+
+    void LayeredEarthEM::SetLayerConductivity(const int& ilay, const Complex &sig) {
+        if (ilay > this->NumberOfLayers || ilay < 1 )
+            throw EarthModelParametersDoNotMatchNumberOfLayers( );
+        LayerConductivity[ilay] = sig;
+    }
+
+/*
+    void LayeredEarthEM::SetLayerResistivity(const VectorXcr &rhos) {
+        if (rhos.size() != this->NumberOfLayers )
+            throw EarthModelParametersDoNotMatchNumberOfLayers( );
+        LayerConductivity = 1./rhos.array();
+    }
+*/
+
+    void LayeredEarthEM::SetLayerHighFreqSusceptibility(const VectorXr &sus) {
+        if (sus.size() != this->NumberOfLayers )
+            throw EarthModelParametersDoNotMatchNumberOfLayers( );
+        LayerHighFreqSusceptibility = sus;
+    }
+
+    void LayeredEarthEM::SetLayerLowFreqSusceptibility(const VectorXr &sus) {
+        if (sus.size() != this->NumberOfLayers )
+            throw EarthModelParametersDoNotMatchNumberOfLayers( );
+        LayerLowFreqSusceptibility = sus;
+    }
+
+    void LayeredEarthEM::SetLayerBreathSusceptibility(const VectorXr &sus) {
+        if (sus.size() != this->NumberOfLayers )
+            throw EarthModelParametersDoNotMatchNumberOfLayers( );
+        LayerBreathSusceptibility = sus;
+    }
+
+    void LayeredEarthEM::SetLayerTauSusceptibility(const VectorXr &sus) {
+        if (sus.size() != this->NumberOfLayers )
+            throw EarthModelParametersDoNotMatchNumberOfLayers( );
+        LayerTauSusceptibility = sus;
+    }
+
+    void LayeredEarthEM::SetLayerHighFreqPermitivity(const VectorXr &per) {
+        if (per.size() != this->NumberOfLayers )
+            throw EarthModelParametersDoNotMatchNumberOfLayers( );
+        LayerHighFreqPermitivity = per;
+    }
+
+    void LayeredEarthEM::SetLayerLowFreqPermitivity(const VectorXr &per) {
+        if (per.size() != this->NumberOfLayers )
+            throw EarthModelParametersDoNotMatchNumberOfLayers( );
+        LayerLowFreqPermitivity = per;
+    }
+
+    void LayeredEarthEM::SetLayerBreathPermitivity(const VectorXr &per) {
+        if (per.size() != this->NumberOfLayers )
+            throw EarthModelParametersDoNotMatchNumberOfLayers( );
+        LayerBreathPermitivity = per;
+    }
+
+    void LayeredEarthEM::SetLayerTauPermitivity(const VectorXr &per) {
+        if (per.size() != this->NumberOfLayers )
+            throw EarthModelParametersDoNotMatchNumberOfLayers( );
+        LayerTauPermitivity = per;
+    }
+
+    void LayeredEarthEM::SetLayerThickness(const VectorXr &thick) {
+        if (thick.size() != this->NumberOfLayers - 2)
+            throw EarthModelParametersDoNotMatchNumberOfLayers( );
+        LayerThickness = thick;
+    }
+
+    void LayeredEarthEM::SetNumberOfLayers(const int&nlay) {
+
+        // Check for validity
+        if (nlay < 2) {
+            throw EarthModelWithLessThanTwoLayers();
+        }
+        //else if (nlay > MAXLAYERS)
+        //    throw EarthModelWithMoreThanMaxLayers();
+
+        // Otherwise
+        this->NumberOfLayers = nlay;
+
+
+        // Resize all layers
+
+        //////////////////////////////////
+        // Thicknesses set to zero
+        LayerThickness = VectorXr::Zero(NumberOfLayers);
+
+
+        ///////////////////////////////////
+        // Conducitivy set to zero
+        LayerConductivity = VectorXcr::Zero(NumberOfLayers);
+
+
+        ////////////////////////////////////
+        // Susceptibility set to One (free space)
+        LayerSusceptibility = VectorXcr::Ones(NumberOfLayers);
+
+        // workaround for Valgrind on AMD which compains about assignment to 1 of VectorXr
+        LayerLowFreqSusceptibility = LayerSusceptibility.real();  // 1
+        LayerHighFreqSusceptibility = LayerSusceptibility.real(); // 1
+        LayerTauSusceptibility = LayerSusceptibility.imag();      // 0
+        LayerBreathSusceptibility = LayerSusceptibility.imag();   // 0
+
+        //////////////////////////////////////
+        // Permitivity set to 1 (free space)
+        //this->LayerPermitivity.resize(NumberOfLayers);
+        //this->LayerPermitivity.setOnes();
+        LayerPermitivity = VectorXcr::Ones(NumberOfLayers);
+
+        // workaround for Valgrind on AMD which compains about assignment to 1 of VectorXr
+        LayerLowFreqPermitivity = LayerPermitivity.real();      // 1
+        LayerHighFreqPermitivity = LayerPermitivity.real();     // 1
+        LayerTauPermitivity = LayerPermitivity.imag();          // 0
+        LayerBreathPermitivity = LayerPermitivity.imag();       // 0
+
+    }
+
+    // ====================  INQUIRY       ===================================
+
+    VectorXcr LayeredEarthEM::GetLayerConductivity() {
+        return this->LayerConductivity;
+    }
+
+    Complex LayeredEarthEM::GetLayerConductivity(const int &ilay) {
+        return this->LayerConductivity(ilay);
+    }
+
+    Complex LayeredEarthEM::GetLayerSusceptibility(const int &ilay) {
+        return this->LayerSusceptibility(ilay);
+    }
+
+    VectorXcr LayeredEarthEM::GetLayerSusceptibility( ) {
+        return this->LayerSusceptibility;
+    }
+
+    Complex LayeredEarthEM::GetLayerPermitivity(const int &ilay) {
+        return this->LayerPermitivity(ilay);
+    }
+
+    VectorXcr LayeredEarthEM::GetLayerPermitivity( ) {
+        return this->LayerPermitivity;
+    }
+
+    Real LayeredEarthEM::GetLayerLowFreqSusceptibility(const int &ilay) {
+        return this->LayerLowFreqSusceptibility(ilay);
+    }
+
+    VectorXr LayeredEarthEM::GetLayerLowFreqSusceptibility( ) {
+        return this->LayerLowFreqSusceptibility;
+    }
+
+    Real LayeredEarthEM::GetLayerHighFreqSusceptibility(const int &ilay) {
+        return this->LayerHighFreqSusceptibility(ilay);
+    }
+
+    VectorXr LayeredEarthEM::GetLayerHighFreqSusceptibility( ) {
+        return this->LayerHighFreqSusceptibility;
+    }
+
+    Real LayeredEarthEM::GetLayerTauSusceptibility(const int &ilay) {
+        return this->LayerTauSusceptibility(ilay);
+    }
+
+    VectorXr LayeredEarthEM::GetLayerTauSusceptibility( ) {
+        return this->LayerTauSusceptibility;
+    }
+
+    Real LayeredEarthEM::GetLayerBreathSusceptibility(const int &ilay) {
+        return this->LayerBreathSusceptibility(ilay);
+    }
+
+    VectorXr LayeredEarthEM::GetLayerBreathSusceptibility( ) {
+        return this->LayerBreathSusceptibility;
+    }
+
+    Real LayeredEarthEM::GetLayerLowFreqPermitivity(const int &ilay) {
+        return this->LayerLowFreqPermitivity(ilay);
+    }
+
+    VectorXr LayeredEarthEM::GetLayerLowFreqPermitivity( ) {
+        return this->LayerLowFreqPermitivity;
+    }
+
+    Real LayeredEarthEM::GetLayerHighFreqPermitivity(const int &ilay) {
+        return this->LayerHighFreqPermitivity(ilay);
+    }
+
+    VectorXr LayeredEarthEM::GetLayerHighFreqPermitivity( ) {
+        return this->LayerHighFreqPermitivity;
+    }
+
+    Real LayeredEarthEM::GetLayerTauPermitivity(const int &ilay) {
+        return this->LayerTauPermitivity(ilay);
+    }
+
+    VectorXr LayeredEarthEM::GetLayerTauPermitivity( ) {
+        return this->LayerTauPermitivity;
+    }
+
+    Real LayeredEarthEM::GetLayerBreathPermitivity(const int &ilay) {
+        return this->LayerBreathPermitivity(ilay);
+    }
+
+    VectorXr LayeredEarthEM::GetLayerBreathPermitivity( ) {
+        return this->LayerBreathPermitivity;
+    }
+}

Modules/FDEM1D/src/modelreaderfem1d.cpp

@@ -0,0 +1,48 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     01/23/2013
+  @version  $Id$
+ **/
+
+#include "modelreaderfem1d.h"
+
+namespace Lemma {
+
+	std::ostream &operator<<(std::ostream &stream,
+		const ModelReaderFem1D &ob) {
+		stream << *(ModelReaderFem1D*)(&ob);
+		return stream;
+	}
+
+	ModelReaderFem1D::ModelReaderFem1D(const std::string &name) :
+		ModelReader(name) {
+	}
+
+	ModelReaderFem1D::~ModelReaderFem1D() {
+		if (NumberOfReferences != 0) {
+			throw DeleteObjectWithReferences(this);
+		}
+	}
+
+	ModelReaderFem1D* ModelReaderFem1D::New() {
+		ModelReaderFem1D* Obj = new ModelReaderFem1D("ModelReaderFem1D");
+		Obj->AttachTo(Obj);
+		return Obj;
+	}
+
+	void ModelReaderFem1D::Delete() {
+		this->DetachFrom(this);
+	}
+
+	void ModelReaderFem1D::Release() {
+		delete this;
+	}
+
+} // end of namespace Lemma

Modules/FDEM1D/src/receivercubes.cpp

@@ -0,0 +1,115 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     06/17/2010
+  @version  $Id: receivercubes.cpp 87 2013-09-05 22:44:05Z tirons $
+ **/
+
+#include "receivercubes.h"
+
+namespace Lemma{
+
+	// ====================    FRIENDS     ======================
+	std::ostream &operator<<(std::ostream &stream,
+				const ReceiverCubes &ob) {
+		stream << *(ReceiverPoints*)(&ob);
+  		return stream;
+	}
+
+	// ====================  LIFECYCLE     ===================================
+
+	ReceiverCubes * ReceiverCubes::New() {
+		ReceiverCubes* Obj = new ReceiverCubes("ReceiverCubes");
+        Obj->AttachTo(Obj);
+        return Obj;
+	}
+
+	void ReceiverCubes::Delete() {
+		this->DetachFrom(this);
+	}
+
+    void ReceiverCubes::Release() {
+		delete this;
+	}
+
+	ReceiverCubes::ReceiverCubes(const std::string &name) :
+			ReceiverPoints(name) {
+	}
+
+	ReceiverCubes::~ReceiverCubes() {
+        if (this->NumberOfReferences != 0)
+            throw DeleteObjectWithReferences( this );
+    }
+
+	// ====================  OPERATIONS    =======================
+
+	void ReceiverCubes::SetNumberOfReceivers(const int &nrec){
+
+        ReceiverPoints::SetNumberOfReceivers(nrec);
+
+		this->Locations.resize(Eigen::NoChange, nrec);
+		this->Locations.setZero();
+
+		this->Lengths.resize(Eigen::NoChange, nrec);
+		this->Lengths.setZero();
+
+	}
+
+	void ReceiverCubes::SetLengthX(const int &ir, const  Real& lx) {
+		this->Lengths.col(ir)[0] = lx;
+	}
+
+	void ReceiverCubes::SetLengthY(const int &ir, const  Real& ly) {
+		this->Lengths.col(ir)[1] = ly;
+	}
+
+	void ReceiverCubes::SetLengthZ(const int &ir, const  Real& lz) {
+		this->Lengths.col(ir)[2] = lz;
+	}
+
+	void ReceiverCubes::SetLength(const int &ir, const  Vector3r& l) {
+		this->Lengths.col(ir) = l;
+	}
+
+	void ReceiverCubes::SetLength(const int &ir,const  Real& lx,
+					const Real& ly, const Real& lz) {
+		this->Lengths.col(ir) << lx, ly, lz;
+	}
+
+	Real ReceiverCubes::GetLengthX(const int &ir) {
+		return this->Lengths.col(ir)[0];
+	}
+
+	Real ReceiverCubes::GetLengthY(const int &ir) {
+		return this->Lengths.col(ir)[1];
+	}
+
+	Real ReceiverCubes::GetLengthZ(const int &ir) {
+		return this->Lengths.col(ir)[2];
+	}
+
+	Vector3r ReceiverCubes::GetLength(const int& ir) {
+		return this->Lengths.col(ir);
+	}
+
+	Real ReceiverCubes::GetVolume(const int& ir) {
+		return this->Lengths.col(ir)[0] *
+			   this->Lengths.col(ir)[1] *
+		       this->Lengths.col(ir)[2] ;
+	}
+
+	Real ReceiverCubes::GetVolumeSum() {
+		Real Vol = 0.;
+		for (int i=0; i<NumberOfReceivers; ++i) {
+			Vol += GetVolume(i);
+		}
+		return Vol;
+	}
+
+}		// -----  end of Lemma  name  -----

Modules/FDEM1D/src/receiverpoints.cpp

@@ -0,0 +1,563 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     12/02/2009
+  @version  $Id: receiverpoints.cpp 203 2015-01-09 21:19:04Z tirons $
+ **/
+
+#include "receiverpoints.h"
+
+namespace Lemma {
+
+    // ====================    FRIENDS     ======================
+
+#ifdef HAVE_YAMLCPP
+    std::ostream &operator << (std::ostream &stream, const ReceiverPoints &ob) {
+        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
+        return stream;
+    }
+#else
+    std::ostream &operator<<(std::ostream &stream,
+                const ReceiverPoints &ob) {
+
+        stream << *(LemmaObject*)(&ob);
+        stream << "Number of Receivers "<< ob.NumberOfReceivers  << "\n";
+        return stream;
+    }
+#endif
+
+    // ====================  LIFECYCLE     ===================================
+
+    ReceiverPoints::ReceiverPoints(const std::string& name) :
+        LemmaObject(name),
+        NumberOfReceivers(0), NumberOfBinsE(0), NumberOfBinsH(0) {
+    }
+
+#ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  ReceiverPoints
+    //      Method:  ReceiverPoints
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    ReceiverPoints::ReceiverPoints (const YAML::Node& node) : LemmaObject(node) {
+
+        //DeSerialize
+        NumberOfReceivers = node["NumberOfReceivers"].as<int>();
+        NumberOfBinsE = node["NumberOfBinsE"].as<int>();
+        NumberOfBinsH = node["NumberOfBinsH"].as<int>();
+        Mask = node["Mask"].as<VectorXi>();
+        Locations = node["Locations"].as<Vector3Xr>();
+
+    }  // -----  end of method ReceiverPoints::ReceiverPoints  (constructor)  -----
+#endif
+
+    ReceiverPoints::~ReceiverPoints() {
+        if (this->NumberOfReferences != 0)
+            throw DeleteObjectWithReferences( this );
+    }
+
+    ReceiverPoints* ReceiverPoints::New() {
+        ReceiverPoints* Obj = new ReceiverPoints("ReceiverPoints");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    void ReceiverPoints::Delete() {
+        this->DetachFrom(this);
+    }
+
+    void ReceiverPoints::Release() {
+        delete this;
+    }
+
+    // ====================  ACCESS        ===================================
+
+    void ReceiverPoints::SetNumberOfReceivers(const int &nrec) {
+
+        if (nrec > 0)
+            this->NumberOfReceivers = nrec;
+        else
+            throw std::runtime_error("NUMBER RECEIVERS LESS THAN 1");
+
+        this->Locations.resize(Eigen::NoChange, nrec);
+        Locations.setZero();
+
+        this->Mask.resize(nrec);
+        Mask.setZero();
+
+        ResizeEField();
+        ResizeHField();
+    }
+
+    void ReceiverPoints::ResizeEField() {
+        Efield.clear();
+        for (int i=0; i<NumberOfBinsE; ++i) {
+            Eigen::Matrix<Complex, 3, Eigen::Dynamic> tempe;
+            this->Efield.push_back(tempe);
+            this->Efield[i].resize(Eigen::NoChange, NumberOfReceivers);
+            this->Efield[i].setZero();
+        }
+    }
+
+    void ReceiverPoints::ResizeHField() {
+        Hfield.clear();
+        for (int i=0; i<NumberOfBinsH; ++i) {
+            Eigen::Matrix<Complex, 3, Eigen::Dynamic> temph;
+            this->Hfield.push_back(temph);
+            this->Hfield[i].resize(Eigen::NoChange, NumberOfReceivers);
+            this->Hfield[i].setZero();
+        }
+    }
+
+    void ReceiverPoints::SetNumberOfBinsE(const int& nbins) {
+        NumberOfBinsE = nbins;
+        ResizeEField();
+    }
+
+    void ReceiverPoints::SetNumberOfBinsH(const int& nbins) {
+        NumberOfBinsH = nbins;
+        ResizeHField();
+    }
+
+    void ReceiverPoints::SetLocation(const int&nrec,const  Vector3r& loc) {
+        this->Locations.col(nrec) = loc;
+    }
+
+    void ReceiverPoints::SetLocation(const int&nrec,const  Real& xp,
+                    const Real& yp, const Real& zp) {
+        this->Locations.col(nrec) << xp, yp, zp;
+    }
+
+    void ReceiverPoints::SetEfield(const int& nbin,
+                    const int& loc, const Complex &ex,
+                    const Complex &ey, const Complex &ez) {
+        this->Efield[nbin].col(loc) << ex, ey, ez;
+    }
+
+    void ReceiverPoints::AppendEfield(const int&nbin, const int& loc,
+                    const Complex &ex,
+                    const Complex &ey, const Complex &ez) {
+        #ifdef LEMMAUSEOMP
+        #pragma omp critical
+        #endif
+        this->Efield[nbin].col(loc) += Vector3cr(ex, ey, ez); //temp;
+    }
+
+    void ReceiverPoints::SetHfield(const int &nbin, const int& loc,
+                    const Complex &hx, const Complex &hy,
+                    const Complex &hz) {
+        this->Hfield[nbin].col(loc) << hx, hy, hz;
+    }
+
+    void ReceiverPoints::AppendHfield(const int &nbin, const int& loc,
+                    const Complex &hx, const Complex &hy,
+                    const Complex &hz) {
+//      #ifdef LEMMAUSEOMP
+//      #pragma omp atomic
+//      std::real(this->Hfield[nbin].col(loc)[0]) += std::real(hx);
+//      #pragma omp atomic
+//      std::imag(this->Hfield[nbin].col(loc)[0]) += std::imag(hx);
+//      #pragma omp atomic
+//      std::real(this->Hfield[nbin].col(loc)[1]) += std::real(hy);
+//      #pragma omp atomic
+//      std::imag(this->Hfield[nbin].col(loc)[1]) += std::imag(hy);
+//      #pragma omp atomic
+//      std::real(this->Hfield[nbin].col(loc)[2]) += std::real(hz);
+//      #pragma omp atomic
+//      std::imag(this->Hfield[nbin].col(loc)[2]) += std::imag(hz);
+//          #else
+        //(critical sections are slow)
+        #ifdef LEMMAUSEOMP
+        #pragma omp critical
+        #endif
+        this->Hfield[nbin].col(loc) += Vector3cr(hx,hy,hz);
+        //#endif
+    }
+
+
+    // ====================  INQUIRY       ===================================
+    Vector3Xr ReceiverPoints::GetLocations() {
+        return this->Locations;
+    }
+
+    MatrixXr ReceiverPoints::GetLocationsMat() {
+        return MatrixXr(this->Locations);
+    }
+
+    Vector3r ReceiverPoints::GetLocation(const int &nrec) {
+        return this->Locations.col(nrec);
+    }
+
+    Real ReceiverPoints::GetLocationX(const int &nrec) {
+        return this->Locations.col(nrec)[0];
+    }
+
+    Real ReceiverPoints::GetLocationY(const int &nrec) {
+        return this->Locations.col(nrec)[1];
+    }
+
+    Real ReceiverPoints::GetLocationZ(const int &nrec) {
+        return this->Locations.col(nrec)[2];
+    }
+
+    Vector3cr ReceiverPoints::GetEfield(const int &nfreq, const int&nrec) {
+        return this->Efield[nfreq].col(nrec);
+    }
+
+    Vector3cr ReceiverPoints::GetHfield(const int &nfreq, const int&nrec) {
+        return this->Hfield[nfreq].col(nrec);
+    }
+
+    std::vector<Vector3Xcr> ReceiverPoints::GetHfield( ) {
+        return this->Hfield;
+    }
+
+    std::vector<Vector3Xcr> ReceiverPoints::GetEfield( ) {
+        return this->Efield;
+    }
+
+    Vector3Xcr ReceiverPoints::GetEfield (const int &nfreq) {
+        return this->Efield[nfreq];
+    }
+
+    MatrixXcr ReceiverPoints::GetEfieldMat (const int &nfreq) {
+        return MatrixXcr(this->Efield[nfreq]);
+    }
+
+    MatrixXcr ReceiverPoints::GetHfieldMat (const int &nfreq) {
+        return MatrixXcr(this->Hfield[nfreq]);
+    }
+
+    Vector3Xcr ReceiverPoints::GetHfield (const int &nfreq) {
+        return this->Hfield[nfreq];
+    }
+
+    void ReceiverPoints::MaskPoint(const int& imask) {
+        Mask(imask) = true;
+    }
+
+    void ReceiverPoints::UnMaskPoint(const int& imask) {
+        Mask(imask) = false;
+    }
+
+    void ReceiverPoints::UnMaskAllPoints() {
+        Mask.setZero();
+    }
+
+    int ReceiverPoints::GetMask(const int& i) {
+        return Mask(i);
+    }
+
+    int ReceiverPoints::GetNumberOfReceivers() {
+        return this->NumberOfReceivers;
+    }
+
+    void ReceiverPoints::ClearFields() {
+        for (int i=0; i<NumberOfBinsE; ++i) {
+            this->Efield[i].setZero();
+        }
+        for (int i=0; i<NumberOfBinsH; ++i) {
+            this->Hfield[i].setZero();
+        }
+    }
+
+
+#ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  ReceiverPoints
+    //      Method:  Serialize
+    //--------------------------------------------------------------------------------------
+    YAML::Node  ReceiverPoints::Serialize (  ) const {
+        YAML::Node node = LemmaObject::Serialize(); //static_cast<const LemmaObject*>(this)->Serialize();
+        node.SetTag( this->Name ); // Set Tag after doing parents
+
+        // update here
+        node["NumberOfReceivers"] = NumberOfReceivers;
+        node["NumberOfBinsE"] = NumberOfBinsE;
+        node["NumberOfBinsH"] = NumberOfBinsH;
+        //node["Mask"] = Mask;
+        //std::cout << "Locations.data" << Locations.data()[0] << std::endl;
+        // node["Locations"] = Locations.data(); // HUGE
+        return node;
+    }		// -----  end of method ReceiverPoints::Serialize  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  ReceiverPoints
+    //      Method:  DeSerialize
+    //--------------------------------------------------------------------------------------
+    ReceiverPoints* ReceiverPoints::DeSerialize ( const YAML::Node& node  ) {
+        ReceiverPoints* Object = new ReceiverPoints(node);
+        Object->AttachTo(Object);
+        DESERIALIZECHECK( node, Object )
+        return Object ;
+    }		// -----  end of method ReceiverPoints::DeSerialize  -----
+#endif
+
+
+    #ifdef LEMMAUSEVTK
+    vtkActor* ReceiverPoints::GetVtkGlyphActor(const FIELDTYPE &ftype,
+                    const Real &clip, const Real &scale,
+                    const int &nfreq) {
+
+        vtkArrowSource        *vArrow;
+        vtkGlyph3D            *vGlyph;
+        vtkActor              *vActor;
+        vtkPolyDataMapper     *vPolyMapper;
+        vtkPoints             *vPoints;
+        vtkDoubleArray        *vVects;
+        vtkPolyData           *vPointSet;
+
+        vActor = vtkActor::New();
+        vGlyph = vtkGlyph3D::New();
+        vArrow = vtkArrowSource::New();
+        vPolyMapper = vtkPolyDataMapper::New();
+        vPoints = vtkPoints::New();
+        vPointSet = vtkPolyData::New();
+        vVects = vtkDoubleArray::New();
+
+        vVects->SetNumberOfComponents(3);
+
+        // Make PointData
+        for (int ic=0; ic<NumberOfReceivers; ++ic) {
+
+            Vector3r loc = this->GetLocation(ic);
+
+            vPoints->InsertPoint(ic, loc[0], loc[1],
+                            loc[2]);
+            Vector3r temp;
+            temp.setZero();
+
+            switch (ftype) {
+                case HFIELDREAL:
+                    temp = scale*(GetHfield(nfreq,ic).real());
+                    break;
+                case HFIELDIMAG:
+                    temp = scale*(GetHfield(nfreq,ic).imag());
+                    break;
+                case EFIELDREAL:
+                    temp = scale*(GetEfield(nfreq, ic).real());
+                    break;
+                case EFIELDIMAG:
+                    temp = scale*(GetEfield(nfreq, ic).imag());
+                    break;
+            }
+            if (temp.norm() > clip) {
+                temp /= temp.norm(); // norm
+                temp *= clip;        // clip dimension
+            }
+
+            vVects->InsertTuple3(ic, temp(0), temp(1),
+                            temp(2));
+        }
+
+        vPointSet->SetPoints(vPoints);
+        vPointSet->GetPointData()->SetVectors(vVects);
+        vGlyph->ScalingOn();
+        vGlyph->SetScaleModeToScaleByVector();
+        vGlyph->SetSourceConnection(vArrow->GetOutputPort());
+        vGlyph->SetVectorMode(true);
+        vGlyph->SetVectorModeToUseVector();
+        vGlyph->OrientOn();
+        vGlyph->SetInputData(vPointSet);
+        vPolyMapper->SetInputConnection(vGlyph->GetOutputPort());
+        vActor->SetMapper(vPolyMapper);
+
+        if (vArrow != NULL) {
+            vArrow->Delete();
+            vArrow = NULL;
+        }
+        //if (vActor != NULL) {
+        //  vActor->Delete();
+        //  vActor = NULL;
+        //}
+        if (vPolyMapper != NULL) {
+            vPolyMapper->Delete();
+            vPolyMapper = NULL;
+        }
+        if (vVects != NULL) {
+            vVects->Delete();
+            vVects = NULL;
+        }
+        if (vPointSet != NULL) {
+            vPointSet->Delete();
+            vPointSet = NULL;
+        }
+        if (vPoints != NULL) {
+            vPoints->Delete();
+            vPoints = NULL;
+        }
+        if (vGlyph != NULL) {
+            vGlyph->Delete();
+            vGlyph = NULL;
+        }
+
+        return vActor;
+    }
+
+    vtkDataObject* ReceiverPoints::GetVtkDataObject(const FIELDTYPE &ftype,
+                    const int& nbin,
+                    const int& start, const int& end,
+                    const FIELDCOMPONENT& fcomp,
+                    const SPATIALCOORDINANT &scord) {
+
+        if (start < 0) throw 77;
+        if (end > NumberOfReceivers) throw 78;
+        if (start > end) throw 79;
+
+        int ifc(-1);
+        switch (fcomp) {
+            case XCOMPONENT:
+                ifc = 0;
+                break;
+            case YCOMPONENT:
+                ifc = 1;
+                break;
+            case ZCOMPONENT:
+                ifc = 2;
+                break;
+        }
+
+        int isc(-1);
+        switch (scord) {
+            case XCOORD:
+                isc = 0;
+                break;
+
+            case YCOORD:
+                isc = 1;
+                break;
+
+            case ZCOORD:
+                isc = 2;
+                break;
+        }
+
+        vtkDoubleArray *_data = vtkDoubleArray::New();
+            _data->SetNumberOfComponents(1);
+
+        vtkDoubleArray *_pos = vtkDoubleArray::New();
+            _pos->SetNumberOfComponents(1);
+
+        int id=0;
+        for (int irec=start; irec<end; ++irec) {
+
+            switch (ftype) {
+
+                case HFIELDREAL:
+                    _data->InsertTuple1(id, std::real(Hfield[nbin](ifc, irec)));
+                    break;
+
+                case HFIELDIMAG:
+                    _data->InsertTuple1(id, std::imag(Hfield[nbin](ifc, irec)));
+                    break;
+
+                case EFIELDREAL:
+                    _data->InsertTuple1(id, std::real(Efield[nbin](ifc, irec)));
+                    break;
+
+                case EFIELDIMAG:
+                    _data->InsertTuple1(id, std::imag(Efield[nbin](ifc, irec)));
+                    break;
+            }
+
+            _pos->InsertTuple1(id, Locations(isc, irec));
+            ++id;
+
+        }
+
+        vtkFieldData *_fieldData = vtkFieldData::New();
+            _fieldData->AllocateArrays(2);
+            _fieldData->AddArray(_data);
+            _fieldData->AddArray(_pos);
+
+        vtkDataObject *_dataObject = vtkDataObject::New();
+            _dataObject->SetFieldData(_fieldData);
+
+        _data->Delete();
+        _pos->Delete();
+        _fieldData->Delete();
+
+        return _dataObject;
+    }
+
+    vtkDataObject* ReceiverPoints::GetVtkDataObjectFreq(const FIELDTYPE &ftype,
+                    const int& nrec,
+                    const int& fstart, const int& fend,
+                    const FIELDCOMPONENT& fcomp,
+                    const VectorXr& Freqs) {
+
+        if (fstart < 0) throw 77;
+        //if (fend > NumberOfFrequencies) throw 78;
+        if (fstart > fend) throw 79;
+
+        int ifc(-1);
+        switch (fcomp) {
+            case XCOMPONENT:
+                ifc = 0;
+                break;
+            case YCOMPONENT:
+                ifc = 1;
+                break;
+            case ZCOMPONENT:
+                ifc = 2;
+                break;
+        }
+
+        vtkDoubleArray *_data = vtkDoubleArray::New();
+            _data->SetNumberOfComponents(1);
+
+        vtkDoubleArray *_pos = vtkDoubleArray::New();
+            _pos->SetNumberOfComponents(1);
+
+        int id=0;
+        //std::cout.precision(12);
+        for (int ifreq=fstart; ifreq<fend; ++ifreq) {
+
+            switch (ftype) {
+
+                case HFIELDREAL:
+                    _data->InsertTuple1(id, std::real(Hfield[ifreq](ifc, nrec)));
+                    //std::cout <<  Hfield[ifreq](ifc, nrec) << std::endl;
+                    break;
+
+                case HFIELDIMAG:
+                    _data->InsertTuple1(id, std::imag(Hfield[ifreq](ifc, nrec)));
+                    break;
+
+                case EFIELDREAL:
+                    _data->InsertTuple1(id, std::real(Efield[ifreq](ifc, nrec)));
+                    break;
+
+                case EFIELDIMAG:
+                    _data->InsertTuple1(id, std::imag(Efield[ifreq](ifc, nrec)));
+                    break;
+            }
+
+            _pos->InsertTuple1(id, Freqs[ifreq]);
+            ++id;
+
+        }
+
+        vtkFieldData *_fieldData = vtkFieldData::New();
+            _fieldData->AllocateArrays(2);
+            _fieldData->AddArray(_data);
+            _fieldData->AddArray(_pos);
+
+        vtkDataObject *_dataObject = vtkDataObject::New();
+            _dataObject->SetFieldData(_fieldData);
+
+        _data->Delete();
+        _pos->Delete();
+        _fieldData->Delete();
+
+        return _dataObject;
+    }
+    #endif
+}

Modules/FDEM1D/src/sintransintegrationkernel.cpp

@@ -0,0 +1,103 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     02/08/2011
+  @version  $Id: sintransintegrationkernel.cpp 87 2013-09-05 22:44:05Z tirons $
+ **/
+
+#include "sintransintegrationkernel.h"
+
+namespace Lemma {
+
+    // ====================  FRIENDS       =======================
+
+//     std::ostream &operator<<(std::ostream &stream,
+// 			const DigitalFilterSinTrans &ob) {
+// 		stream << *(DigitalFilterIntegrator<Real>*)(&ob);
+// 		return stream;
+// 	}
+
+    // ====================  LIFECYCLE     =======================
+
+    SinTransIntegrationKernel::
+        SinTransIntegrationKernel(const std::string& name) :
+        IntegrationKernel<Real>(name) {
+    }
+
+    SinTransIntegrationKernel::~SinTransIntegrationKernel() {}
+
+
+    SinTransIntegrationKernel* SinTransIntegrationKernel::New() {
+        SinTransIntegrationKernel* Obj =
+            new SinTransIntegrationKernel("SinTransIntegrationKernel");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    void SinTransIntegrationKernel::Delete() {
+        this->DetachFrom(this);
+    }
+
+    void SinTransIntegrationKernel::Release() {
+        delete this;
+    }
+
+    // ====================  OPERATIONS    =======================
+
+    void SinTransIntegrationKernel::SetA(const Real& Ain) {
+        A = Ain;
+    }
+
+    void SinTransIntegrationKernel::SetIntegral(const int& i) {
+        Integral = i;
+    }
+
+    Real SinTransIntegrationKernel::GetAnalytical (const Real& B) {
+        Real SQPI = std::sqrt(PI);
+        switch (Integral) {
+            case 1:
+                return SQPI*B*std::exp(-B*B/(4.*A*A))/(4.*A*A*A);
+                break;
+            case 2:
+                return (PI/2.)*std::exp(-A*B);
+                break;
+            case 3:
+                return B/(A*A+B*B);
+                break;
+            default:
+                std::cerr << "Test integral is not allowed\n";
+                exit(EXIT_FAILURE);
+        }
+    }
+
+    Real SinTransIntegrationKernel::Argument(const Real&x, const int& iRelated) {
+
+//     1      DEXP(-A*A*G*G)    SQPI*DEXP(-B*B/(4.*A*A))/(2.*A), WHERE
+//                               SQPI="SQUARE ROOT OF PI"
+//     2      1/(A*A+G*G)       (PI/2)*DEXP(-A*B)/A
+//     3      DEXP(-A*G)        A/(A*A+B*B)
+
+        switch (Integral) {
+            case 1:
+                return x*std::exp( -A*A*x*x );
+            case 2:
+                return x/(A*A+x*x);
+            case 3:
+                return std::exp(-A*x);
+            default:
+                std::cerr << "Test integral is not allowed\n";
+                exit(EXIT_FAILURE);
+        }
+    }
+
+    int SinTransIntegrationKernel::GetNumRel( ) {
+        return 1;
+    }
+
+}		// -----  end of Lemma  name  -----

Modules/Optimization/include/quasinewtonbfgs.h

@@ -0,0 +1,111 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     08/09/2010
+  @version  $Id: quasinewtonbfgs.h 193 2014-11-10 23:51:41Z tirons $
+ **/
+
+#ifndef  QUASINEWTONBFGS_INC
+#define  QUASINEWTONBFGS_INC
+
+#include "inversesolver.h"
+
+namespace Lemma {
+
+
+    // ===================================================================
+    //  Class:  QuasiNewtonBFGS
+    /**
+      @class  QuasiNewtonBFGS
+      \brief  Implimentation of a quasi-newton BFGS solver applied to
+              inverse problems.
+      \details Based of the algorithm described in Nocedal and Wright book.
+     */
+    // ===================================================================
+    class QuasiNewtonBFGS : public InverseSolver {
+
+        friend  std::ostream &operator<<(std::ostream &stream,
+                const QuasiNewtonBFGS &ob);
+
+        public:
+
+            // ====================  LIFECYCLE     =======================
+
+            /** Returns a pointer to a new object of type QuasiNewtonBFGS.
+             * It allocates all necessary memory.
+             */
+            static QuasiNewtonBFGS* New();
+
+            /**
+             * @copybrief LemmaObject::Delete()
+             * @copydetails LemmaObject::Delete()
+             */
+            void Delete();
+
+            // ====================  OPERATORS     =======================
+
+            // ====================  OPERATIONS    =======================
+
+            // ====================  ACCESS        =======================
+
+            // ====================  INQUIRY       =======================
+
+            /** @copybrief InverseSolver::NumberOfIterations()
+             *  @copydetails InverseSolver::NumberOfIterations()
+             */
+            int NumberOfIterations();
+
+            /** @copybrief InverseSolver::Success()
+             *  @copydetails InverseSolver::Success()
+             */
+            bool Success();
+
+            /** @copybrief InverseSolver::GetPhiMVector()
+             *  @copydetails InverseSolver::GetPhiMVector()
+             */
+            VectorXr GetPhiMVector();
+
+            /** @copybrief InverseSolver::GetPhiDVector()
+             *  @copydetails InverseSolver::GetPhiDVector()
+             */
+            VectorXr GetPhiDVector();
+
+            /// TODO remove this, test
+            void PrintNorm();
+
+        protected:
+
+            // ====================  LIFECYCLE     =======================
+
+            /// Default protected constructor.
+            QuasiNewtonBFGS (const std::string& cname);
+
+            /// Default protected constructor.
+            ~QuasiNewtonBFGS ();
+
+            /**
+             * @copybrief LemmaObject::Release()
+             * @copydetails LemmaObject::Release()
+             */
+            void Release();
+
+            // ====================  OPERATIONS    =======================
+
+            /// Just a filler
+            void FillInG(const Vector3r& pos, const Vector3r& step);
+
+            // ====================  DATA MEMBERS  =========================
+
+        private:
+
+    }; // -----  end of class  QuasiNewtonBFGS  -----
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef QUASINEWTONBFGS_INC  -----

Modules/Optimization/src/quasinewtonbfgs.cpp

@@ -0,0 +1,85 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   Trevor Irons
+  @date     08/09/2010
+  @version  $Id: quasinewtonbfgs.cpp 87 2013-09-05 22:44:05Z tirons $
+ **/
+
+#include "quasinewtonbfgs.h"
+
+
+namespace Lemma {
+
+    // ====================  STREAMS       =======================
+
+    std::ostream &operator<<(std::ostream &stream,
+            const QuasiNewtonBFGS &ob) {
+        stream << *(InverseSolver*)(&ob);
+        return stream;
+    }
+
+
+    // ====================  LIFECYCLE     =======================
+
+    QuasiNewtonBFGS* QuasiNewtonBFGS::New() {
+        QuasiNewtonBFGS* Object = new QuasiNewtonBFGS("QuasiNewtonBFGS");
+        Object->AttachTo(Object);
+        return Object;
+    }
+
+    QuasiNewtonBFGS::QuasiNewtonBFGS(const std::string &name) :
+        InverseSolver(name) {
+    }
+
+    void QuasiNewtonBFGS::Delete() {
+        this->DetachFrom(this);
+    }
+
+    void QuasiNewtonBFGS::Release() {
+        delete this;
+    }
+
+    QuasiNewtonBFGS::~QuasiNewtonBFGS() {
+        if (this->NumberOfReferences != 0)
+            throw DeleteObjectWithReferences( this );
+    }
+
+    // ====================  INQUIRY       =======================
+
+    int QuasiNewtonBFGS::NumberOfIterations() {
+        return 0;
+    }
+
+    bool QuasiNewtonBFGS::Success () {
+        return false;
+    }
+
+    void QuasiNewtonBFGS::PrintNorm() {
+        std::cout << "Norm " << std::endl;
+        PredictedData->Zero();
+        std::cout << ObservedData->Norm(PredictedData) << std::endl;
+    }
+
+    VectorXr QuasiNewtonBFGS::GetPhiMVector() {
+        VectorXr NewVec(2);
+        return NewVec;
+    }
+
+    VectorXr QuasiNewtonBFGS::GetPhiDVector() {
+        VectorXr NewVec(2);
+        return NewVec;
+    }
+
+    void QuasiNewtonBFGS::FillInG(const Vector3r& pos, const Vector3r& step) {
+
+    }
+
+    // ====================  ACCESS        =======================
+
+}		// -----  end of Lemma  name  -----

Modules/TEM1D/examples/datatem.cpp

@@ -0,0 +1,44 @@
+// ===========================================================================
+//
+//       Filename:
+//
+//    Description:
+//
+//        Version:  0.0
+//        Created:  03/02/2010 02:10:53 PM
+//       Revision:  none
+//       Compiler:  Tested with g++, icpc, and MSVC 2000
+//
+//         Author:  Trevor Irons (ti)
+//
+//   Organisation:  Colorado School of Mines (CSM)
+//                  United States Geological Survey (USGS)
+//
+//          Email:  tirons@mines.edu, tirons@usgs.gov
+//
+//  This program is free software: you can redistribute it and/or modify
+//  it under the terms of the GNU General Public License as published by
+//  the Free Software Foundation, either version 3 of the License, or
+//  (at your option) any later version.
+//
+//  This program is distributed in the hope that it will be useful,
+//  but WITHOUT ANY WARRANTY; without even the implied warranty of
+//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+//  GNU General Public License for more details.
+//
+//  You should have received a copy of the GNU General Public License
+//  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+//
+// ===========================================================================
+
+#include "Lemma"
+using namespace Lemma;
+
+int main() {
+
+	DataTEM * tdata = DataTEM::New();
+	std::cout << *tdata << std::endl;
+	tdata->Zero();
+	tdata->Delete();
+
+}

Modules/TEM1D/include/TEMInductiveReceiver.h

@@ -0,0 +1,106 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      10/08/2014 03:17:52 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+
+#ifndef  TEMINDUCTIVERECEIVER_INC
+#define  TEMINDUCTIVERECEIVER_INC
+
+#include "TEMReceiver.h"
+
+namespace Lemma {
+
+    /**
+      \brief   Derived class of TEMReceiver.
+      \details An inductive receiver, measures dB/dt
+     */
+    class TEMInductiveReceiver : public TEMReceiver {
+
+        friend std::ostream &operator<<(std::ostream &stream,
+                const TEMInductiveReceiver &ob);
+
+        public:
+
+        // ====================  LIFECYCLE     =======================
+
+        /**
+         * @copybrief LemmaObject::New()
+         * @copydetails LemmaObject::New()
+         */
+        static TEMInductiveReceiver* New();
+
+        /**
+         *  @copybrief   LemmaObject::Delete()
+         *  @copydetails LemmaObject::Delete()
+         */
+        void Delete();
+
+        // ====================  OPERATORS     =======================
+
+        // ====================  OPERATIONS    =======================
+
+        // ====================  ACCESS        =======================
+
+        // ====================  INQUIRY       =======================
+
+#ifdef HAVE_YAMLCPP
+        /**
+         *  Uses YAML to serialize this object.
+         *  @return a YAML::Node
+         */
+        YAML::Node Serialize() const;
+
+        /**
+         *   Constructs an object from a YAML::Node.
+         */
+        static TEMInductiveReceiver* DeSerialize(const YAML::Node& node);
+#endif
+
+        protected:
+
+        // ====================  LIFECYCLE     =======================
+
+        /** Default protected constructor, use New */
+        TEMInductiveReceiver (const std::string& name);
+
+#ifdef HAVE_YAMLCPP
+        /** Default protected constructor, use New */
+        TEMInductiveReceiver (const YAML::Node& node);
+#endif
+
+        /** Default protected destructor, use Delete */
+        ~TEMInductiveReceiver ();
+
+        /**
+         *  @copybrief   LemmaObject::Release()
+         *  @copydetails LemmaObject::Release()
+         */
+        void Release();
+
+        private:
+
+        // ====================  DATA MEMBERS  =========================
+
+    }; // -----  end of class  TEMInductiveReceiver  -----
+
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef TEMINDUCTIVERECEIVER_INC  -----
+
+

Modules/TEM1D/include/TEMReceiver.h

@@ -0,0 +1,184 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      10/08/2014 02:36:47 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#ifndef  TEMRECEIVER_INC
+#define  TEMRECEIVER_INC
+
+#include "receiverpoints.h"
+
+//#include <boost/random.hpp>
+//#include <boost/random/normal_distribution.hpp>
+#include <random>
+
+namespace Lemma {
+
+#ifdef HAVE_YAMLCPP
+#include "yaml-cpp/yaml.h"
+#endif
+
+
+/**
+  \brief
+  \details
+ */
+class TEMReceiver : public ReceiverPoints {
+
+    friend std::ostream &operator<<(std::ostream &stream,
+            const TEMReceiver &ob);
+
+    public:
+
+    // ====================  LIFECYCLE     =======================
+
+    /**
+     * @copybrief LemmaObject::New()
+     * @copydetails LemmaObject::New()
+     */
+    static TEMReceiver* New();
+
+    /**
+     *   @return a deep copy of this
+     */
+    TEMReceiver* Clone();
+
+    /**
+     *  @copybrief   LemmaObject::Delete()
+     *  @copydetails LemmaObject::Delete()
+     */
+    void Delete();
+
+    // ====================  OPERATORS     =======================
+
+    // ====================  OPERATIONS    =======================
+
+    /**
+     * Uses the standard deviations provided to provide an instance
+     * of the expected noise. A realisation of the noise.
+     */
+    VectorXr SampleNoise();
+
+    // ====================  ACCESS        =======================
+
+    /**
+     *    Sets the gate integration windows
+     */
+    void SetWindows(const VectorXr& centres, const VectorXr& widths, const TIMEUNITS& Units);
+
+    /**
+     *   Sets the moment of the receiver. Defaults to 1 for normalized response.
+     */
+    void SetMoment( const Real&  moment);
+
+    /**
+     *  Sets std deviation values for noise channels.
+     *  @param[in] noise must be of the same length as the number of windows.
+     */
+    void SetNoiseSTD( const VectorXr& noise );
+
+    /**
+     *  Gets std deviation values for noise channels.
+     *  @return noise std dev.
+     */
+    VectorXr GetNoiseSTD(  );
+
+    /**
+     *  @param[in] refTime sets the reference time, defaults to 0
+     */
+    void SetReferenceTime( const Real& refTime, const TIMEUNITS& units );
+
+    /**
+     *  What field component to return
+     */
+    void SetComponent ( const FIELDCOMPONENT& COMP );
+
+    /**
+     *   @param[in] loc is the location of the dipole receiver
+     */
+    void SetRxLocation ( const Vector3r& loc );
+
+    // ====================  INQUIRY       =======================
+
+     #ifdef HAVE_YAMLCPP
+	/**
+     *  Uses YAML to serialize this object.
+     *  @return a YAML::Node
+     */
+    YAML::Node Serialize() const;
+
+    /**
+     *   Constructs an object from a YAML::Node.
+     */
+    static TEMReceiver* DeSerialize(const YAML::Node& node);
+     #endif
+
+    /**
+     * @return centre point of gates in sec
+     */
+    VectorXr GetWindowCentres();
+
+    /**
+     * @return width of gates in sec
+     */
+    VectorXr GetWindowWidths();
+
+    /**
+     *  @return the reference time
+     */
+    Real    GetReferenceTime();
+    protected:
+
+    // ====================  LIFECYCLE     =======================
+
+    /** Default protected constructor, use New */
+    TEMReceiver (const std::string& name);
+
+     #ifdef HAVE_YAMLCPP
+    /** Default protected de-serializing constructor, use factory DeSerialize */
+    TEMReceiver (const YAML::Node& node);
+    #endif
+
+    /** Default protected destructor, use Delete */
+    ~TEMReceiver ();
+
+    /**
+     *  @copybrief   LemmaObject::Release()
+     *  @copydetails LemmaObject::Release()
+     */
+    void Release();
+
+    private:
+
+    // ====================  DATA MEMBERS  =========================
+
+    Real            moment;
+    Real            referenceTime;
+    Vector3r        nHat;
+    FIELDCOMPONENT  component;
+
+    VectorXr        windowCentres;
+    VectorXr        windowWidths;
+    VectorXr        noiseSTD;
+    //Vector3r        location;
+
+}; // -----  end of class  TEMReceiver  -----
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef TEMRECEIVER_INC  -----
+

Modules/TEM1D/include/TEMSurvey.h

@@ -0,0 +1,137 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      10/08/2014 01:51:50 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#ifndef  TEMSURVEY_INC
+#define  TEMSURVEY_INC
+
+#include "LemmaObject.h"
+#include "TEMSurveyLine.h"
+#include "TEMSurveyData.h"
+
+#include "layeredearthem.h"
+
+#ifdef HAVE_YAMLCPP
+#include "yaml-cpp/yaml.h"
+#endif
+
+namespace Lemma {
+
+
+    /**
+      \brief   Describes a TEM survey.
+      \details This class aims to encapulate any type of TEM survey.
+     */
+    class TEMSurvey : public LemmaObject {
+
+        friend std::ostream &operator<<(std::ostream &stream,
+                const TEMSurvey &ob);
+
+        public:
+
+        // ====================  LIFECYCLE     =======================
+
+        /**
+         * @copybrief LemmaObject::New()
+         * @copydetails LemmaObject::New()
+         */
+        static TEMSurvey* New();
+
+        /**
+         *  @copybrief   LemmaObject::Delete()
+         *  @copydetails LemmaObject::Delete()
+         */
+        void Delete();
+
+        // ====================  OPERATORS     =======================
+
+        /**  @param[in] idx the index to return
+         *   @return the SurveyLine with index idx
+         */
+        TEMSurveyLine* operator( ) ( const int& idx ) const ;
+
+        /**  @param[in] iline the line index to return
+         *   @param[in] irec the line index to return
+         *   @return the SurveyLine with index iline, irec
+         */
+        TEMSurveyLineRecord* operator( ) ( const int& iline, const int& irec ) const;
+
+        // ====================  OPERATIONS    =======================
+
+        /**
+         *  @param[in] nlines sets the number of lines (TEMSurveyLine) in the survey. A line is any kind of
+         *             related set of measurements. In Airborne EM, this is a flight line, but
+         *             the idea extends to ground based profile lines.
+         */
+        void SetNumberOfLines( const int& nlines );
+
+        /**
+         *  Most basic form of forward modelling. Uses input model for ALL TEMSurveyLines and
+         *  TEMSurveyLineRecords (atomic). Most useful in the
+         *  case that there is only 1 line and 1 record. But even in that case it can be called directly from
+         *  the record. This method will likely be replaced  soon.
+         */
+        TEMSurveyData* ForwardModel(LayeredEarthEM* model, bool additiveNoise=false);
+
+        // ====================  ACCESS        =======================
+
+        /**
+         *   @return pointer to requested TEMSurveyLine
+         */
+        TEMSurveyLine*  GetLine(const unsigned int& iline);
+
+        // ====================  INQUIRY       =======================
+
+        #ifdef HAVE_YAMLCPP
+        YAML::Node Serialize() const;
+        static TEMSurvey* DeSerialize(const YAML::Node& node);
+        #endif
+
+        protected:
+
+        // ====================  LIFECYCLE     =======================
+
+        /** Default protected constructor, use New */
+        TEMSurvey (const std::string& name);
+
+        #ifdef HAVE_YAMLCPP
+        /** Default protected constructor, use New */
+        TEMSurvey (const YAML::Node& node);
+        #endif
+
+        /** Default protected destructor, use Delete */
+        ~TEMSurvey ();
+
+        /**
+         *  @copybrief   LemmaObject::Release()
+         *  @copydetails LemmaObject::Release()
+         */
+        void Release();
+
+        private:
+
+        // ====================  DATA MEMBERS  =========================
+
+        std::vector<TEMSurveyLine*>     Lines;
+
+    }; // -----  end of class  TEMSurvey  -----
+
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef TEMSURVEY_INC  -----

Modules/TEM1D/include/TEMSurveyData.h

@@ -0,0 +1,161 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      03/03/2015 09:54:25
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2015, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2015, Trevor Irons
+ */
+
+#ifndef  TEMSURVEYDATA_INC
+#define  TEMSURVEYDATA_INC
+
+#include "LemmaObject.h"
+#include "TEMSurveyLineData.h"
+
+namespace Lemma {
+
+    /**
+      \brief    Holds data from a TEMSurvey.
+      \details  Any form of TEMSurvey may be represented here. The
+                majority of the specification can be found in the associated
+                TEMSurvey. The TEMSurveyData object is intended to be lightweight.
+     */
+    class TEMSurveyData : public LemmaObject {
+
+        friend std::ostream &operator<<(std::ostream &stream,
+                const TEMSurveyData &ob);
+
+        friend class TEMSurvey;
+
+        public:
+
+        // ====================  LIFECYCLE     =======================
+
+        /**
+         * @copybrief LemmaObject::New()
+         * @copydetails LemmaObject::New()
+         */
+        static TEMSurveyData* New();
+
+        /**
+         *  @return a deep copy of this, this is acomplished through Serialize
+         *          and DeSerialize methods.
+         */
+        TEMSurveyData* Clone();
+
+        /**
+         *  @copybrief   LemmaObject::Delete()
+         *  @copydetails LemmaObject::Delete()
+         */
+        void Delete();
+
+        // ====================  OPERATORS     =======================
+
+        /** Surveys can be added or subtracted from each other, throws a
+         *  pointer that will need to be managed (Deleted)
+         */
+        TEMSurveyData* operator+(const TEMSurveyData& Survey);
+
+        /** Surveys can be added or subtracted from each other, throws a
+         *  pointer that will need to be managed (Deleted).
+         */
+        TEMSurveyData* operator-(const TEMSurveyData& Survey);
+
+        /** Surveys can be added or subtracted from each other
+         */
+        void operator+=(const TEMSurveyData& Survey);
+
+        /** Surveys can be added or subtracted from each other
+         */
+        void operator-=(const TEMSurveyData& Survey);
+
+
+        /**  @param[in] idx the index to return
+         *   @return the SurveyLine with index idx
+         */
+        TEMSurveyLineData* operator( ) ( const int& idx ) const;
+
+        /**  @param[in] iline the line index to return
+         *   @param[in] irec the line index to return
+         *   @return the SurveyLine with index iline, irec
+         */
+        TEMSurveyLineRecordData* operator( ) ( const int& iline, const int& irec ) const;
+
+
+        // ====================  OPERATIONS    =======================
+
+        /** Sets the number of lines
+         */
+        void SetNumberOfLines( const int& nlines );
+
+        // ====================  ACCESS        =======================
+
+        /** @return the number of lines in the data
+         */
+        int GetNumberOfLines() const;
+
+        /**
+         *   @return pointer to line
+         */
+        TEMSurveyLineData* GetLine(const int& iline) const;
+
+        // ====================  INQUIRY       =======================
+
+#ifdef HAVE_YAMLCPP
+        /**
+         *  Uses YAML to serialize this object.
+         *  @return a YAML::Node
+         */
+        YAML::Node Serialize() const;
+
+        /**
+         *   Constructs an object from a YAML::Node.
+         */
+        static TEMSurveyData* DeSerialize(const YAML::Node& node);
+#endif
+
+        protected:
+
+        // ====================  LIFECYCLE     =======================
+
+        /** Default protected constructor, use New */
+        TEMSurveyData (const std::string& name);
+
+#ifdef HAVE_YAMLCPP
+        /** Protected DeDerializing constructor, use factory DeSerialize  method*/
+        TEMSurveyData (const YAML::Node& node);
+#endif
+
+        /** Default protected destructor, use Delete */
+        ~TEMSurveyData ();
+
+        /**
+         *  @copybrief   LemmaObject::Release()
+         *  @copydetails LemmaObject::Release()
+         */
+        void Release();
+
+        private:
+
+        // ====================  DATA MEMBERS  =========================
+
+        std::vector<TEMSurveyLineData*>  LineData;
+
+    }; // -----  end of class  TEMSurveyData  -----
+
+
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef TEMSURVEYDATA_INC  -----

Modules/TEM1D/include/TEMSurveyLine.h

@@ -0,0 +1,117 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      10/10/2014 11:14:39 AM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#ifndef  TEMSURVEYLINE_INC
+#define  TEMSURVEYLINE_INC
+
+#include "LemmaObject.h"
+#include "TEMSurveyLineRecord.h"
+#include "TEMSurveyLineData.h"
+
+namespace Lemma {
+
+    /**
+      \brief    Represents a TEM survey line.
+      \details  This class is managed by TEMSurvey. You cannot create a TEMSurvey line directly
+                this should be done through a TEMSurvey.
+                @todo neeed to impliment a BaseClass besides LemmaObject without pure virtual Delete.
+     */
+    class TEMSurveyLine : public LemmaObject {
+
+        friend std::ostream &operator<<(std::ostream &stream,
+                const TEMSurveyLine &ob);
+
+        friend class TEMSurvey;
+
+        public:
+
+        // ====================  LIFECYCLE     =======================
+
+
+
+        // ====================  OPERATORS     =======================
+
+        // ====================  OPERATIONS    =======================
+
+        // ====================  ACCESS        =======================
+
+        /**
+            @return returns pointer to a specific record along the line
+         */
+        TEMSurveyLineRecord*  GetRecord(const unsigned int& irec);
+
+        /**
+            @param[in] nrec is the number of records along the line
+         */
+        void SetNumberOfRecords( const int& nrec );
+
+        // ====================  INQUIRY       =======================
+
+#ifdef HAVE_YAMLCPP
+        /**
+         *  Uses YAML to serialize this object.
+         *  @return a YAML::Node
+         */
+        YAML::Node Serialize() const;
+
+        /**
+         *   Constructs an object from a YAML::Node.
+         */
+        static TEMSurveyLine* DeSerialize(const YAML::Node& node);
+#endif
+
+        protected:
+
+        TEMSurveyLineData* ForwardModel(LayeredEarthEM* model, bool additiveNoise = false);
+
+        // ====================  LIFECYCLE     =======================
+
+        /** Default protected constructor, use New */
+        TEMSurveyLine (const std::string& name);
+
+#ifdef HAVE_YAMLCPP
+        /** Protected DeDerializing constructor, use factory DeSerialize  method*/
+        TEMSurveyLine (const YAML::Node& node);
+#endif
+
+        /** Default protected destructor, use Delete */
+        ~TEMSurveyLine ();
+
+        /**
+         *  @copybrief   LemmaObject::Release()
+         *  @copydetails LemmaObject::Release()
+         */
+        void Release();
+
+        private:
+
+        /**
+         *   Delete should not be called...
+         */
+        void Delete();
+
+        // ====================  DATA MEMBERS  =========================
+
+        std::vector<TEMSurveyLineRecord*>     Records;
+
+    }; // -----  end of class  TEMSurveyLine  -----
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef TEMSURVEYLINE_INC  -----

Modules/TEM1D/include/TEMSurveyLineData.h

@@ -0,0 +1,146 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      03/03/2015 10:16:47
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2015, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2015, Trevor Irons
+ */
+
+#ifndef  TEMSURVEYLINEDATA_INC
+#define  TEMSURVEYLINEDATA_INC
+
+#include "LemmaObject.h"
+#include "TEMSurveyLineRecordData.h"
+
+namespace Lemma {
+
+/**
+  \brief   Holds Data for a TEM survey line
+  \details An entire flight line worth of data is stored here.
+ */
+class TEMSurveyLineData : public LemmaObject {
+
+    friend std::ostream &operator<<(std::ostream &stream,
+            const TEMSurveyLineData &ob);
+
+    //friend class TEMSurveyData;
+    friend class TEMSurveyLine;
+
+    public:
+
+    // ====================  LIFECYCLE     =======================
+
+    /**
+     * @copybrief LemmaObject::New()
+     * @copydetails LemmaObject::New()
+     */
+    static TEMSurveyLineData* New();
+
+    /**
+     *  @return a deep copy of this, this is acomplished through Serialize
+     *          and DeSerialize methods.
+     */
+    TEMSurveyLineData* Clone();
+
+    /**
+     *  @copybrief   LemmaObject::Delete()
+     *  @copydetails LemmaObject::Delete()
+     */
+    void Delete();
+
+    // ====================  OPERATORS     =======================
+
+    /** Survey lines can be added or subtracted from each other
+     */
+    TEMSurveyLineData* operator+(const TEMSurveyLineData& Survey);
+
+    /** Survey lines can be added or subtracted from each other
+     */
+    TEMSurveyLineData* operator-(const TEMSurveyLineData& Survey);
+
+    /** Survey lines can be added or subtracted from each other
+     */
+    void operator+=(const TEMSurveyLineData& Survey);
+
+    /** Survey lines can be added or subtracted from each other
+     */
+    void operator-=(const TEMSurveyLineData& Survey);
+
+    /**  @param[in] ir the index to return
+     *   @return the SurveyLineRecord with index ir
+     */
+    TEMSurveyLineRecordData* operator( ) ( const int& ir ) const ;
+
+    // ====================  OPERATIONS    =======================
+
+    // ====================  ACCESS        =======================
+
+    /**
+     *    @return pointer to specified record
+     */
+    TEMSurveyLineRecordData*  GetRecord(const int& ir) const ;
+
+    /**
+     * @return the number of records
+     */
+    int GetNumberOfRecords() const;
+
+    // ====================  INQUIRY       =======================
+
+#ifdef HAVE_YAMLCPP
+    /**
+     *  Uses YAML to serialize this object.
+     *  @return a YAML::Node
+     */
+    YAML::Node Serialize() const;
+
+    /**
+     *   Constructs an object from a YAML::Node.
+     */
+    static TEMSurveyLineData* DeSerialize(const YAML::Node& node);
+#endif
+
+    protected:
+
+    // ====================  LIFECYCLE     =======================
+
+    /** Default protected constructor, use New */
+    TEMSurveyLineData (const std::string& name);
+
+#ifdef HAVE_YAMLCPP
+    /** Protected DeDerializing constructor, use factory DeSerialize  method*/
+    TEMSurveyLineData (const YAML::Node& node);
+#endif
+
+    /** Default protected destructor, use Delete */
+    ~TEMSurveyLineData ();
+
+    /**
+     *  @copybrief   LemmaObject::Release()
+     *  @copydetails LemmaObject::Release()
+     */
+    void Release();
+
+    private:
+
+    // ====================  DATA MEMBERS  =========================
+
+    std::vector<TEMSurveyLineRecordData*>   RecordData;
+
+}; // -----  end of class  TEMSurveyLineData  -----
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef TEMSURVEYLINEDATA_INC  -----
+

Modules/TEM1D/include/TEMSurveyLineRecord.h

@@ -0,0 +1,140 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      10/10/2014 12:15:03 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#ifndef  TEMSURVEYLINERECORD_INC
+#define  TEMSURVEYLINERECORD_INC
+
+#include "LemmaObject.h"
+#include "TEMReceiver.h"
+#include "TEMTransmitter.h"
+#include "TEMSurveyLineRecordData.h"
+#include "instrumenttem.h"
+
+namespace Lemma {
+
+    /**
+      \brief    Class holding everything necessary to create a TEM record.
+      \details  A TEM record represents the nexus of a transmitter with
+                receiver(s) and pulse moment(s). Therefore a record can contain
+                multiple sounding curves.
+     */
+    class TEMSurveyLineRecord : public LemmaObject {
+
+        friend std::ostream &operator<<(std::ostream &stream,
+                const TEMSurveyLineRecord &ob);
+
+        friend class TEMSurveyLine;
+
+        public:
+
+        // ====================  LIFECYCLE     =======================
+
+        // ====================  OPERATORS     =======================
+
+        // ====================  OPERATIONS    =======================
+
+        /**
+         *  Perfoms forward modelling given model.
+         *  @param[in] model is the earth model responsible for the response
+         *  @param[in] additiveNoise is whether or not to add noise to the response, defaults to false
+         *  @return the modelled data.
+         */
+        TEMSurveyLineRecordData* ForwardModel(LayeredEarthEM* model, bool additiveNoise=false);
+
+        /**
+         *  @param[in] nseq is the number of pulse sequences
+         */
+        void SetNumberOfPulseSequences( const int& nseq );
+
+        /**
+         *  @return the number of pulse sequences
+         */
+        int GetNumberOfPulseSequences();
+
+        /**
+         *  Sets the PulseSequence and Receiver pair used to model a *SINGLE* response curve.
+         *  @param[in] Seq is the Pulse Sequence
+         *  @param[in] Rx is the receiver for that pulse sequence
+         */
+        void SetTransmitterReceiverPair( const int& ii, TEMTransmitter* Seq, TEMReceiver* Rx );
+
+        // ====================  ACCESS        =======================
+
+        /**
+         *  @return a pointer to the specified receiver
+         */
+        TEMReceiver*   GetReceiver(const int& irec);
+
+        // ====================  INQUIRY       =======================
+
+#ifdef HAVE_YAMLCPP
+        /**
+         *  Uses YAML to serialize this object.
+         *  @return a YAML::Node
+         */
+        YAML::Node Serialize() const;
+
+        /**
+         *   Constructs an object from a YAML::Node.
+         */
+        static TEMSurveyLineRecord* DeSerialize(const YAML::Node& node);
+#endif
+
+        protected:
+
+
+
+        // ====================  LIFECYCLE     =======================
+
+        /** Default protected constructor, use New */
+        TEMSurveyLineRecord (const std::string& name);
+
+#ifdef HAVE_YAMLCPP
+        /** Protected DeDerializing constructor, use factory DeSerialize  method*/
+        TEMSurveyLineRecord (const YAML::Node& node);
+#endif
+
+        /** Default protected destructor, use Delete */
+        ~TEMSurveyLineRecord ();
+
+        /**
+         *  @copybrief   LemmaObject::Release()
+         *  @copydetails LemmaObject::Release()
+         */
+        void Release();
+
+        private:
+
+        /**
+         *   Delete is private, this class is managed through TEMSurvey
+         */
+        void Delete();
+
+        // ====================  DATA MEMBERS  =========================
+
+        int     numberOfPulseSequences;
+
+        std::vector<TEMTransmitter*>    Transmitters;
+        std::vector<TEMReceiver*>       Receivers;
+
+    }; // -----  end of class  TEMSurveyLineRecord  -----
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef TEMSURVEYLINERECORD_INC  -----

Modules/TEM1D/include/TEMSurveyLineRecordData.h

@@ -0,0 +1,141 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      03/03/2015 10:29:01
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2015, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2015, Trevor Irons
+ */
+#ifndef  TEMSURVEYLINERECORDDATA_INC
+#define  TEMSURVEYLINERECORDDATA_INC
+
+#include "LemmaObject.h"
+
+namespace Lemma {
+
+    /**
+      \brief
+      \details
+     */
+    class TEMSurveyLineRecordData : public LemmaObject {
+
+        friend std::ostream &operator<<(std::ostream &stream,
+                const TEMSurveyLineRecordData &ob);
+
+        friend class TEMSurveyLineRecord;
+
+        public:
+
+        // ====================  LIFECYCLE     =======================
+
+        /**
+         * @copybrief LemmaObject::New()
+         * @copydetails LemmaObject::New()
+         */
+        static TEMSurveyLineRecordData* New();
+
+
+        /** Provides deep copy
+         */
+        TEMSurveyLineRecordData* Clone();
+
+        /**
+         *  @copybrief   LemmaObject::Delete()
+         *  @copydetails LemmaObject::Delete()
+         */
+        void Delete();
+
+        // ====================  OPERATORS     =======================
+
+        /**
+         * Records can be added
+         */
+        TEMSurveyLineRecordData* operator + (const TEMSurveyLineRecordData&);
+
+        /**
+         * Records can be subtracted
+         */
+        TEMSurveyLineRecordData* operator - (const TEMSurveyLineRecordData&);
+
+        /**
+         * Records can be added in place
+         */
+        void operator += (const TEMSurveyLineRecordData&);
+
+        /**
+         * Records can be subtracted in place
+         */
+        void operator -= (const TEMSurveyLineRecordData&);
+
+        // ====================  OPERATIONS    =======================
+
+        // ====================  ACCESS        =======================
+
+        /** @return a VectorXr of the merged data (all moments)
+         * @todo TODO this is actually a copy? is this intended?
+         */
+        VectorXr GetCombinedData();
+
+        /** @return a VectorXr of the combined gate centres alligned with
+         *          GetCombinedData();
+         */
+        VectorXr GetCombinedGateCentres();
+        // ====================  INQUIRY       =======================
+
+#ifdef HAVE_YAMLCPP
+        /**
+         *  Uses YAML to serialize this object.
+         *  @return a YAML::Node
+         */
+        YAML::Node Serialize() const;
+
+        /**
+         *   Constructs an object from a YAML::Node.
+         */
+        static TEMSurveyLineRecordData* DeSerialize(const YAML::Node& node);
+#endif
+
+        protected:
+
+        // ====================  LIFECYCLE     =======================
+
+        /** Default protected constructor, use New */
+        TEMSurveyLineRecordData (const std::string& name);
+
+#ifdef HAVE_YAMLCPP
+        /** Protected DeDerializing constructor, use factory DeSerialize  method*/
+        TEMSurveyLineRecordData (const YAML::Node& node);
+#endif
+
+        /** Default protected destructor, use Delete */
+        ~TEMSurveyLineRecordData ();
+
+        /**
+         *  @copybrief   LemmaObject::Release()
+         *  @copydetails LemmaObject::Release()
+         */
+        void Release();
+
+        private:
+
+        // ====================  DATA MEMBERS  =========================
+
+        std::vector<VectorXr>           DataSeries;
+
+        std::vector<VectorXr>           GateCentres;
+
+    }; // -----  end of class  TEMSurveyLineRecordData  -----
+
+}		// -----  end of Lemma  name  -----
+
+#endif   // ----- #ifndef TEMSURVEYLINERECORDDATA_INC  -----

Modules/TEM1D/include/TEMTransmitter.h

@@ -0,0 +1,125 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      09/29/2014 11:43:17 AM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#ifndef  TEMTRANSMITTER_INC
+#define  TEMTRANSMITTER_INC
+
+#include "PolygonalWireAntenna.h"
+
+#ifdef HAVE_YAMLCPP
+#include "yaml-cpp/yaml.h"
+#endif
+
+namespace Lemma {
+
+/**
+  \brief   Describes a TEM pulse sequence
+  \details Flexible class desribing a pulse sequence used by
+           a TEM instruement. Can be used by Airborne or Ground
+           instruments.
+ */
+class TEMTransmitter : public PolygonalWireAntenna {
+
+    friend std::ostream &operator<<(std::ostream &stream, const TEMTransmitter &ob);
+
+    public:
+
+    // ====================  LIFECYCLE     =======================
+
+    /**
+     * @copybrief LemmaObject::New()
+     * @copydetails LemmaObject::New()
+     */
+    static TEMTransmitter* New();
+
+    /**
+     *  Performs a deep copy of this and returns pointer
+     */
+    TEMTransmitter* Clone();
+
+    /**
+     *  @copybrief   LemmaObject::Delete()
+     *  @copydetails LemmaObject::Delete()
+     */
+    void Delete();
+
+    // ====================  OPERATORS     =======================
+
+    // ====================  OPERATIONS    =======================
+
+    // ====================  ACCESS        =======================
+
+    /** Sets the repetition frequency
+     */
+    void SetRepFrequency(const Real& fr, const FREQUENCYUNITS& units);
+
+    void SetWaveform( const VectorXr& times, const VectorXr& amps, const TIMEUNITS& units );
+
+    /**
+     *  @return the waveform times in seconds
+     */
+    VectorXr GetWfmTimes();
+
+    /** @return the waveform current in amps
+     */
+    VectorXr GetWfmAmps();
+
+    // ====================  INQUIRY       =======================
+
+#ifdef HAVE_YAMLCPP
+    YAML::Node Serialize() const;
+    static TEMTransmitter* DeSerialize(const YAML::Node& node);
+#endif
+
+    protected:
+
+    // ====================  LIFECYCLE     =======================
+
+    /** Default protected constructor, use New */
+    TEMTransmitter (const std::string& name);
+
+#ifdef HAVE_YAMLCPP
+    /** Default protected constructor, use New */
+    TEMTransmitter (const YAML::Node& node);
+#endif
+
+    /** Default protected destructor, use Delete */
+    ~TEMTransmitter ();
+
+    /**
+     *  @copybrief   LemmaObject::Release()
+     *  @copydetails LemmaObject::Release()
+     */
+    void Release();
+
+    private:
+
+    // ====================  DATA MEMBERS  =========================
+
+    Real                    repFreq;
+    FREQUENCYUNITS          repFreqUnits;
+    VectorXr                wfmTimes;
+    VectorXr                wfmAmps;
+
+}; // -----  end of class  TEMTransmitter  -----
+
+} // namespace Lemma
+
+#endif   // ----- #ifndef TEMTRANSMITTER_INC  -----
+

Modules/TEM1D/include/instrumenttem.h

@@ -0,0 +1,213 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   M. Andy Kass
+  @date     02/10/2011
+  @version  $Id: instrumenttem.h 201 2015-01-03 00:07:47Z tirons $
+ **/
+
+#ifndef __INSTRUMENTTEM_H
+#define __INSTRUMENTTEM_H
+
+#include "instrument.h"
+#include "emearth1d.h"
+#include "WireAntenna.h"
+#include "PolygonalWireAntenna.h"
+#include "receiverpoints.h"
+#include "dipolesource.h"
+#include "layeredearthem.h"
+#include "digitalfiltercostrans.h"
+#include "digitalfiltersintrans.h"
+#include "temintegrationkernel.h"
+#include "CubicSplineInterpolator.h"
+
+namespace Lemma {
+
+enum ReceiverType { INDUCTIVE, MAGNETOMETER, ELECTRIC };
+
+// ===================================================================
+//        Class:  InstrumentTem
+/// \brief  TEM Instrument Class
+/// \details Provides utility to forward model TEM data in Lemma.
+// ===================================================================
+class InstrumentTem : public Instrument {
+
+	friend std::ostream &operator<<(std::ostream &stream,
+		const InstrumentTem &ob);
+
+	public:
+
+	// ====================  LIFECYCLE     =======================
+
+		static InstrumentTem* New();
+
+		void Delete();
+
+	// ====================  OPERATORS     =======================
+
+	// ====================  OPERATIONS    =======================
+
+		/// Perform the forward model calculation
+		void MakeDirectCalculation( const HANKELTRANSFORMTYPE& hType );
+
+        /** Perform the forward model calculation, use lagged convolutions to
+         *  speed up the calculations
+         */
+		void MakeLaggedCalculation( const HANKELTRANSFORMTYPE& hType );
+
+	// ====================  ACCESS        =======================
+
+		/** Sets pulse parameters as a linearly segmented graph, so
+         *  for example a triangle wave needs three points in Amps and
+         *  times, a trapazoidal needs for. The pulse is assumed (defaults) to be
+         *  bipolar, only the positive polarity should be specified.
+         *  @param[in] Amp is the waveform current in Amps
+         *  @param[in] times are the abscissa values of the waveform
+         *  @param[in] bipolar specifies whether or not the pulse is bipolar
+         */
+		void SetPulse( const VectorXr& Amp, const VectorXr& times, bool bipolar=true );
+
+		/// Sets layered earth model
+		void EMEarthModel(LayeredEarthEM* Earth);
+
+		/// Sets transmitter parameters
+		void SetTransmitLoop(WireAntenna *antennae);
+
+		/// Sets dipole source parameters
+		void SetDipoleSource(DipoleSource* dipolesource);
+
+		/// Sets receiver points and parameters
+		void SetReceiver(ReceiverPoints* Receivers);
+
+        /** Sets the type of receiver/measurement
+         */
+        void SetReceiverType( const ReceiverType& rtype  );
+
+		/// Return calculated data
+		MatrixXr GetMeasurements();
+
+		/**
+            Set time gates, assumes gates widths are delta (instantaneous)
+            @param[in] times gate centres units are in seconds
+         */
+
+		void SetTimes(const VectorXr &times);
+
+        /** Sets time gates centres and widths, both in seconds. The window is assumed to be
+         *  a simple boxcar. Simpson's rule is used to integrate the response
+         * @param[in] times gate centres units are in seconds
+         * @param[in] widths gate widths units are in seconds
+         */
+        void SetTimeGates(const VectorXr &centres, const VectorXr& widths);
+
+		/// Get number of times
+		int GetNumberOfTimes();
+
+        /** Sets reference time for time gate to pulse time offset.
+         */
+        void SetReferenceTime(const Real& RefTime);
+
+		/// Attach EMEarth1D
+		//void AttachEMEarth1D(EMEarth1D *EMEarth);
+
+	// ====================  INQUIRY       =======================
+
+
+
+	protected:
+
+	// ====================  LIFECYCLE     =======================
+
+		/// Default protected constructor.
+		InstrumentTem (const std::string &name);
+
+		/// Default protected constructor.
+		~InstrumentTem ();
+
+		void Release();
+
+    // ====================  OPERATIONS    =======================
+
+        /**
+         *  Converts impulse B response (step db/dt) into inductive db/dt
+         *  response for general waveform.
+         */
+        void FoldAndConvolve( CubicSplineInterpolator* Spline );
+
+        /** Convolves the transmitter waveform(s), takes the impulse response
+            and uses simpson's rule to evaluate the integral.
+            @param[in] Spline is the Cubic Spline object representing the solution.
+            @param[in] t is the evaluation time.
+         */
+        Real ConvolveWaveform( CubicSplineInterpolator* Spline, const Real& t );
+
+        /** Subtracts previous waveform(s) from current impulse response, and re-splines.
+         */
+        void SubtractPrevious( CubicSplineInterpolator* Spline );
+
+
+	// ====================  DATA MEMBERS  =========================
+
+		//EMEarth1D* EmEarth;
+
+		WireAntenna* Antenna;
+
+		ReceiverPoints* Receiver;
+
+		LayeredEarthEM* EarthMod;
+
+		DipoleSource* Dipole;
+
+        bool     bipolarWaveform;
+
+        /** Number of previous pules to model */
+        int      NPreviousPulse;
+
+        /** Reference time (relative to pulse abscissa) for time gates */
+        Real     RefTime;
+
+        /** Pulse period, if bimodal 1/2 repitition period */
+        Real     PulseT;
+
+        /** Transmitter repitition frequency */
+        Real     TxFreq;
+
+        /** Receiver type */
+        ReceiverType  RType;
+
+        MatrixXr ModelledData;
+
+        /** Centre of time gate */
+		VectorXr TimeGates;
+
+        /** Width of time gates */
+        VectorXr GateWidths;
+
+        /** Pulse waveform */
+        VectorXr Waveform;
+
+        /** Current Amplitude of pulse */
+        VectorXr  TxAmp;
+
+        /** Current -delta of pulse */
+        VectorXr  TxDelta;
+
+        /** Current derivative of pulse */
+        VectorXr  TxDiff;
+
+        /** times associated with TxAmp segments */
+        VectorXr  TxAbs;
+
+	private:
+
+}; // -----  end of class  InstrumentTem  -----
+
+} // End of namespace Lemma
+
+#endif // __TEMINSTRUMENT_H
+

Modules/TEM1D/include/inversesolvertem1d.h

@@ -0,0 +1,146 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   M. Andy Kass
+  @date     03/23/2011
+  @version  $Id: inversesolvertem1d.h 201 2015-01-03 00:07:47Z tirons $
+ **/
+
+#ifndef _INVERSESOLVERTEM1D__H
+#define _INVERSESOLVERTEM1D__H
+
+#include "inversesolver.h"
+#include "layeredearthem.h"
+#include "WireAntenna.h"
+#include "dipolesource.h"
+#include "receiverpoints.h"
+#include "instrumenttem.h"
+#include "cg.h"
+
+namespace Lemma {
+	// ===================================================================
+	//        Class:  InverseSolverTEM1D
+	/// \brief  Inversion for 1D TEM data
+	/// \details
+	// ===================================================================
+	class InverseSolverTEM1D : public InverseSolver {
+
+		friend std::ostream &operator<<(std::ostream &stream,
+			const InverseSolverTEM1D &ob);
+
+		public:
+
+		// ====================  LIFECYCLE     =======================
+
+		static InverseSolverTEM1D* New();
+
+		void Delete();
+
+		// ====================  OPERATORS     =======================
+
+		// ====================  OPERATIONS    =======================
+
+		/// Perform the inverse calculation
+		void Calculate();
+
+		// ====================  ACCESS        =======================
+
+		/// Attach starting model
+		void AttachStartMod(LayeredEarthEM* inpstartmod);
+
+		/// Attach recovered model
+		void AttachRecMod(LayeredEarthEM* inprecmod);
+
+		/// Attach wire antenna source
+		void AttachWireAntenna(WireAntenna* inpwireantenna);
+
+		/// Attach dipole source
+		void AttachDipoleSource(DipoleSource* inpdipsource);
+
+		/// Attach receiver points
+		void AttachReceiver(ReceiverPoints* inpreceiver);
+
+		/// Set the time gates
+		void SetTimes(VectorXr &inptimes);
+
+		/// Show forward modelled data
+		void ShowSoln();
+
+		/// Write recovered model to file
+		void WriteSoln(const std::string &filename);
+
+		/// Set free parameter indices: layer, conductivity
+		void SetFreeParams(const VectorXi &layers, const VectorXi &cond);
+
+		/// Attach measured data for misfit comparison
+		void AttachMeasuredData(const MatrixXr &data);
+
+		// ====================  INQUIRY       =======================
+		/// Report number of iterations
+		int NumberOfIterations();
+
+		/// Report success/failure
+		bool Success();
+
+		/// Return phi m vector
+		VectorXr GetPhiMVector();
+
+		/// Return phi d vector
+		VectorXr GetPhiDVector();
+
+
+		protected:
+
+		/// Some crap trevor uses
+		void FillInG(const Vector3r& pos, const Vector3r& step);
+
+		/// Calculate Jacobian
+		MatrixXr CalcJac(LayeredEarthEM* m0);
+
+		// ====================  LIFECYCLE     =======================
+
+		/// Default protected constructor.
+		InverseSolverTEM1D (const std::string &name);
+
+		/// Default protected constructor.
+		~InverseSolverTEM1D ();
+
+        void Release();
+
+		// ====================  DATA MEMBERS  =========================
+
+		WireAntenna* Antenna;
+
+		DipoleSource* Dipole;
+
+		ReceiverPoints* Receiver;
+
+		LayeredEarthEM* StartingMod;
+
+		LayeredEarthEM* RecoveredMod;
+
+		InstrumentTem *InstrumentFor;
+
+		MatrixXr MeasuredData;
+
+		VectorXr Times;
+
+		/// Vector of indices for which layer conductivities are solved for
+		VectorXi SCondIndex;
+
+		/// Vecor of indices for which layer thicknesses are solved for
+		VectorXi SThickIndex;
+
+		/// Temporary vector for returning linearised step
+		VectorXr RecModStep;
+
+		private:
+
+}; // -----  end of class  InverseSolverTEM1D  -----
+} // End of namespace Lemma
+#endif // _INVERSESOLVERTEM1D__H

Modules/TEM1D/include/modelreadertem1d.h

@@ -0,0 +1,83 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   M. Andy Kass
+  @date     02/19/2011
+  @version  $Id: modelreadertem1d.h 87 2013-09-05 22:44:05Z tirons $
+ **/
+
+#ifndef __MODELREADERTEM1D_H
+#define __MODELREADERTEM1D_H
+
+#include "modelreader.h"
+
+namespace Lemma {
+
+// ===================================================================
+//        Class:  ModelReaderTem1D
+/// \brief Model reader class for forward modelling 1D TEM data
+/// \details This is a mostly abstract class.
+// ===================================================================
+class ModelReaderTem1D : public ModelReader {
+
+	friend std::ostream &operator<<(std::ostream &stream,
+		const ModelReaderTem1D &ob);
+
+	public:
+
+		// ====================  LIFECYCLE     =======================
+
+		static ModelReaderTem1D* New();
+
+		void Delete();
+
+		// ====================  OPERATORS     =======================
+
+		// ====================  OPERATIONS    =======================
+
+		//void ReadParameters(/* Pass file name */);
+
+		// ====================  ACCESS        =======================
+
+		// ====================  INQUIRY       =======================
+
+
+	protected:
+
+		// ====================  LIFECYCLE     =======================
+
+		/// Default protected constructor.
+		ModelReaderTem1D (const std::string &name);
+
+		/// Default protected constructor.
+		~ModelReaderTem1D ();
+
+		void Release();
+
+		/// Read in the Earth Model file and attach
+		//void ReadModel();
+
+		/// Read in the instrument parameters and attach
+		//void ReadInstrument();
+
+		/// Read in the waveform file (future)
+		//void ReadWaveform();
+
+		// ====================  DATA MEMBERS  =========================
+
+		//std::string modelfile;
+
+		//std::string instrumentfile;
+
+		//std::string waveformfile;
+
+	private:
+
+}; // -----  end of class  ModelReaderTem1D  -----
+} // end of namespace lemma
+#endif // __MODELREADERTEM1D_H

Modules/TEM1D/include/modelreadertem1dubc.h

@@ -0,0 +1,116 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   M. Andy Kass
+  @date     02/19/2011
+  @version  $Id: modelreadertem1dubc.h 87 2013-09-05 22:44:05Z tirons $
+ **/
+
+#ifndef __MODELREADERTEM1DUBC_H
+#define __MODELREADERTEM1DUBC_H
+
+#include "modelreadertem1d.h"
+
+namespace Lemma {
+
+// ===================================================================
+//        Class:  ModelReaderTem1DUBC
+/// \brief Model reader class for forward modelling 1D TEM data
+/// \details Reads UBC 1D TEM forward model format
+// ===================================================================
+class ModelReaderTem1DUBC : public ModelReaderTem1D {
+
+	friend std::ostream &operator<<(std::ostream &stream,
+		const ModelReaderTem1DUBC &ob);
+
+	public:
+
+		// ====================  LIFECYCLE     =======================
+
+		static ModelReaderTem1DUBC* New();
+
+		void Delete();
+
+		// ====================  OPERATORS     =======================
+
+		// ====================  OPERATIONS    =======================
+
+		void ReadParameters(const std::string &params);
+
+		// ====================  ACCESS        =======================
+
+		/// Attaches a LayeredEarthEM object
+		void SetEMEarth1D(LayeredEarthEM* earth);
+
+		/// Attaches a WireAntenna object
+		void SetTransmitter(WireAntenna *antennae);
+
+		/// Attaches a ReceiverPoints object
+		void SetReceiver(ReceiverPoints* receiver);
+
+		VectorXr GetTimes();
+
+		// ====================  INQUIRY       =======================
+
+
+	protected:
+
+		// ====================  LIFECYCLE     =======================
+
+		/// Default protected constructor.
+		ModelReaderTem1DUBC (const std::string &name);
+
+		/// Default protected constructor.
+		~ModelReaderTem1DUBC ();
+
+		void Release();
+
+		/// Read in the Earth Model file and attach
+		void ReadModel();
+
+		/// Read in the instrument parameters and attach
+		void ReadInstrument();
+
+		/// Read in the waveform file (future)
+		void ReadWaveform();
+
+		// ====================  DATA MEMBERS  =========================
+
+		std::string modelfile;
+
+		std::string instrumentfile;
+
+		std::string waveformfile;
+
+		WireAntenna* Trans;
+
+		ReceiverPoints* Receivers;
+
+		LayeredEarthEM* EarthMod;
+
+		/// Simulated noise flag
+		bool addednoise;
+
+		/// Simulated noise percentage
+		Real noisepercent;
+
+		/// Baseline threshold percentage
+		Real noisethresh;
+
+		/// Seed for random number generator
+		Real noiseseed;
+
+		VectorXr receivermoment;
+
+		VectorXr modtimes;
+
+	private:
+
+}; // -----  end of class  ModelReaderTem1DUBC  -----
+} // end of namespace lemma
+#endif // __MODELREADERTEM1DUBC_H

Modules/TEM1D/include/temintegrationkernel.h

@@ -0,0 +1,103 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   M. Andy Kass
+  @date     02/10/2011
+  @version  $Id: temintegrationkernel.h 190 2014-10-16 23:02:09Z tirons $
+ **/
+
+#ifndef __TEMINTEGRATIONKERNEL_H
+#define __TEMINTEGRATIONKERNEL_H
+
+#include "integrationkernel.h"
+#include "emearth1d.h"
+
+namespace Lemma {
+
+
+// ===================================================================
+//        Class:  TemIntegrationKernel
+/// \brief  Integration kernel for calculation of TEM data
+/// \details Calculates the integration kernel for the sine transform
+// ===================================================================
+
+class TemIntegrationKernel : public IntegrationKernel<Real>{
+
+	//friend std::ostream &operator<<(std::ostream &stream,
+	//	const TemIntegrationKernel &ob);
+
+	public:
+
+	// ====================  LIFECYCLE     =======================
+
+		static TemIntegrationKernel* New();
+
+		void Delete();
+
+	// ====================  OPERATORS     =======================
+
+	// ====================  OPERATIONS    =======================
+
+	// ====================  ACCESS        =======================
+
+		/// Calculates the integration argument.  Passed a frequency.
+		Real Argument(const Real&x, const int& iRelated);
+
+		int GetNumRel();
+
+		/// Attach EMEarth1D object to TemIntegrationKernel
+		void SetEMEarth1D(EMEarth1D* earth);
+
+		/// Attach Transmitter object
+		void SetTransmitter(WireAntenna *antennae);
+
+		/// Attach Dipole object
+		void SetDipole(DipoleSource* dipolesource);
+
+		/// Attach Receiver object
+		void SetReceiver(ReceiverPoints *receiver);
+
+        /**
+         *   @param[in] comp is the component to integrate
+         */
+        void SetComponent(const FIELDCOMPONENT& comp);
+	// ====================  INQUIRY       =======================
+
+
+
+	protected:
+
+	// ====================  LIFECYCLE     =======================
+
+		/// Default protected constructor.
+		TemIntegrationKernel (const std::string& name);
+
+		/// Default protected constructor.
+		~TemIntegrationKernel ();
+
+		void Release();
+
+	// ====================  DATA MEMBERS  =========================
+
+        FIELDCOMPONENT  component;
+
+		EMEarth1D* EmEarthInt;
+
+		WireAntenna* Trans;
+
+		DipoleSource* DipoleS;
+
+		ReceiverPoints* Receivers;
+
+	private:
+
+}; // -----  end of class  TemIntegrationKernel  -----
+
+} // End of namespace Lemma
+
+#endif // __TEMINTEGRATIONKERNEL_H

Modules/TEM1D/src/TEMInductiveReceiver.cpp

@@ -0,0 +1,127 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      10/08/2014 03:19:58 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#include "TEMInductiveReceiver.h"
+
+namespace Lemma {
+
+
+
+    // ====================  FRIEND METHODS  =====================
+#ifdef HAVE_YAMLCPP
+    std::ostream &operator << (std::ostream &stream, const TEMInductiveReceiver &ob) {
+        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
+        return stream;
+    }
+#else
+    std::ostream &operator<<(std::ostream &stream, const TEMInductiveReceiver& ob) {
+        stream << *(TEMReceiver*)(&ob);
+        return stream;
+    }
+#endif
+
+    // ====================  LIFECYCLE     =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMInductiveReceiver
+    //      Method:  TEMInductiveReceiver
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMInductiveReceiver::TEMInductiveReceiver (const std::string& name) : TEMReceiver(name) {
+
+    }  // -----  end of method TEMInductiveReceiver::TEMInductiveReceiver  (constructor)  -----
+
+#ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMInductiveReceiver
+    //      Method:  TEMInductiveReceiver
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMInductiveReceiver::TEMInductiveReceiver (const YAML::Node& node) : TEMReceiver(node) {
+
+    }  // -----  end of method TEMInductiveReceiver::TEMInductiveReceiver  (constructor)  -----
+#endif
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMInductiveReceiver
+    //      Method:  New()
+    // Description:  public constructor
+    //--------------------------------------------------------------------------------------
+    TEMInductiveReceiver* TEMInductiveReceiver::New() {
+        TEMInductiveReceiver*  Obj = new TEMInductiveReceiver("TEMInductiveReceiver");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMInductiveReceiver
+    //      Method:  ~TEMInductiveReceiver
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMInductiveReceiver::~TEMInductiveReceiver () {
+
+    }  // -----  end of method TEMInductiveReceiver::~TEMInductiveReceiver  (destructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMInductiveReceiver
+    //      Method:  Delete
+    // Description:  public destructor
+    //--------------------------------------------------------------------------------------
+    void TEMInductiveReceiver::Delete() {
+        this->DetachFrom(this);
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMInductiveReceiver
+    //      Method:  Release
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    void TEMInductiveReceiver::Release() {
+        delete this;
+    }
+
+
+#ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMInductiveReceiver
+    //      Method:  Serialize
+    //--------------------------------------------------------------------------------------
+    YAML::Node  TEMInductiveReceiver::Serialize (  ) const {
+        YAML::Node node;
+        node = TEMReceiver::Serialize();
+        node.SetTag( this->Name ); // Set Tag after doing parents
+        return node;
+    }		// -----  end of method TEMInductiveReceiver::Serialize  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMInductiveReceiver
+    //      Method:  DeSerialize
+    //--------------------------------------------------------------------------------------
+    TEMInductiveReceiver* TEMInductiveReceiver::DeSerialize ( const YAML::Node& node  ) {
+        TEMInductiveReceiver* Object = new TEMInductiveReceiver(node);
+        Object->AttachTo(Object);
+        DESERIALIZECHECK( node, Object )
+        return Object ;
+    }		// -----  end of method TEMInductiveReceiver::DeSerialize  -----
+#endif
+
+
+}		// -----  end of Lemma  name  -----
+

Modules/TEM1D/src/TEMReceiver.cpp

@@ -0,0 +1,333 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      10/08/2014 03:04:56 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#include "TEMReceiver.h"
+
+namespace Lemma {
+
+
+    // ====================  FRIEND METHODS  =====================
+#ifdef HAVE_YAMLCPP
+    std::ostream &operator << (std::ostream &stream, const TEMReceiver &ob) {
+        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
+        return stream;
+    }
+#else
+    std::ostream &operator<<(std::ostream &stream, const TEMReceiver& ob) {
+        stream << *(ReceiverPoints*)(&ob);
+        return stream;
+    }
+#endif
+
+    // ====================  LIFECYCLE     =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  TEMReceiver
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMReceiver::TEMReceiver (const std::string& name) : ReceiverPoints(name), moment(1), referenceTime(0) {
+
+    }  // -----  end of method TEMReceiver::TEMReceiver  (constructor)  -----
+
+#ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  TEMReceiver
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMReceiver::TEMReceiver (const YAML::Node& node) : ReceiverPoints(node) {
+
+        moment = node["moment"].as<Real>();
+        referenceTime = node["referenceTime"].as<Real>();
+        component = string2Enum<FIELDCOMPONENT>( node["component"].as<std::string>() );
+
+        windowCentres = node["windowCentres"].as<VectorXr>();
+        windowWidths  = node["windowWidths"].as<VectorXr>();
+        noiseSTD      = node["noiseSTD"].as<VectorXr>();
+        //location = node["location"].as<Vector3r>();
+    }  // -----  end of method TEMReceiver::TEMReceiver  (constructor)  -----
+#endif
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  New()
+    // Description:  public constructor
+    //--------------------------------------------------------------------------------------
+    TEMReceiver* TEMReceiver::New() {
+        TEMReceiver*  Obj = new TEMReceiver("TEMReceiver");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  Clone
+    //--------------------------------------------------------------------------------------
+    TEMReceiver* TEMReceiver::Clone() {
+        TEMReceiver* Copy = TEMReceiver::New();
+            Copy->SetNumberOfReceivers( this->NumberOfReceivers );
+            Copy->Mask = this->Mask;
+            Copy->Locations = this->Locations;
+            // TEM stuff
+            Copy->moment = this->moment;
+            Copy->referenceTime = this->referenceTime;
+            Copy->nHat = this->nHat;
+            Copy->component = this->component;
+            Copy->windowCentres = this->windowCentres;
+            Copy->windowWidths = this->windowWidths;
+            Copy->noiseSTD = this->noiseSTD;
+        return Copy;
+    }		// -----  end of method TEMReceiver::Clone  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  ~TEMReceiver
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMReceiver::~TEMReceiver () {
+
+    }  // -----  end of method TEMReceiver::~TEMReceiver  (destructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  Delete
+    // Description:  public destructor
+    //--------------------------------------------------------------------------------------
+    void TEMReceiver::Delete() {
+        this->DetachFrom(this);
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  Release
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    void TEMReceiver::Release() {
+        delete this;
+    }
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  SetWindows
+    //--------------------------------------------------------------------------------------
+    void TEMReceiver::SetWindows ( const VectorXr& centres, const VectorXr& widths, const TIMEUNITS& Units ) {
+
+        Real sc(0);
+        switch (Units) {
+            case SEC:
+                sc = 1;
+                break;
+            case MILLISEC:
+                sc = 1e-3;
+                break;
+            case MICROSEC:
+                sc = 1e-6;
+                break;
+            case NANOSEC:
+                sc = 1e-9;
+                break;
+            case PICOSEC:
+                sc = 1e-12;
+                break;
+        };
+        windowCentres = sc*centres;
+        windowWidths = sc*widths;
+        noiseSTD = VectorXr::Zero(windowCentres.size());
+        return ;
+    }		// -----  end of method TEMReceiver::SetWindows  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  SetNoiseSTD
+    //--------------------------------------------------------------------------------------
+    void TEMReceiver::SetNoiseSTD ( const VectorXr& noiseIn ) {
+        if ( noiseIn.size() == windowCentres.size() ) {
+            noiseSTD = noiseIn;
+        } else {
+            throw std::runtime_error("TEMReceiver::SetNoiseSTD not aligned");
+        }
+        return ;
+
+    }		// -----  end of method TEMReceiver::SetNoiseSTD  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  GetNoiseSTD
+    //--------------------------------------------------------------------------------------
+    VectorXr TEMReceiver::GetNoiseSTD (  ) {
+        return noiseSTD ;
+    }		// -----  end of method TEMReceiver::GetNoiseSTD  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  SampleNoise
+    //--------------------------------------------------------------------------------------
+    VectorXr TEMReceiver::SampleNoise (  ) {
+        
+	/* we have C++-11 now! No Boost! 
+        boost::mt19937 rng(time(0));
+        boost::normal_distribution<> nd(0.0, 1.0);
+        boost::variate_generator<boost::mt19937&, boost::normal_distribution<> > var_nor(rng, nd);
+	*/
+
+        std::random_device rd;
+        std::mt19937 gen(rd()); 
+        std::normal_distribution<> d(0.0, 1.00);
+
+        VectorXr noise = VectorXr::Zero( windowCentres.size() );
+        for (int ii=0; ii<windowCentres.size(); ++ii) {
+            //noise(ii) = var_nor(); // old boost way
+            noise(ii) = d(gen);
+        }
+        return noise.array() * noiseSTD.array();
+    }		// -----  end of method TEMReceiver::SampleNoise  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  SetReferenceTime
+    //--------------------------------------------------------------------------------------
+    void TEMReceiver::SetReferenceTime ( const Real& refTime, const TIMEUNITS& units ) {
+        Real sc(0);
+        switch (units) {
+            case SEC:
+                sc = 1;
+                break;
+            case MILLISEC:
+                sc = 1e-3;
+                break;
+            case MICROSEC:
+                sc = 1e-6;
+                break;
+            case NANOSEC:
+                sc = 1e-9;
+                break;
+            case PICOSEC:
+                sc = 1e-12;
+                break;
+        };
+        referenceTime = sc*refTime;
+
+        return ;
+    }		// -----  end of method TEMReceiver::SetReferenceTime  -----
+
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  SetMoment
+    //--------------------------------------------------------------------------------------
+    void TEMReceiver::SetMoment ( const Real& mom ) {
+        moment = mom;
+        return ;
+    }		// -----  end of method TEMReceiver::SetMoment  -----
+
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  SetLocation
+    //--------------------------------------------------------------------------------------
+    void TEMReceiver::SetRxLocation ( const Vector3r& loc ) {
+        this->SetNumberOfReceivers(1); // Valgrind doesn't like??
+        this->SetLocation(0, loc);
+        //location = loc;
+        return ;
+    }		// -----  end of method TEMReceiver::SetLocation  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  SetComponent
+    //--------------------------------------------------------------------------------------
+    void TEMReceiver::SetComponent ( const FIELDCOMPONENT& comp  ) {
+        component = comp;
+        return ;
+    }		// -----  end of method TEMReceiver::SetComponent  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  get_WindowWidths
+    //--------------------------------------------------------------------------------------
+    VectorXr TEMReceiver::GetWindowWidths (  ) {
+        return windowWidths;
+    }		// -----  end of method TEMReceiver::get_WindowWidths  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  get_WindowCentres
+    //--------------------------------------------------------------------------------------
+    VectorXr TEMReceiver::GetWindowCentres (  ) {
+        return windowCentres;
+    }		// -----  end of method TEMReceiver::get_WindowCentres  -----
+
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  GetReferenceTime
+    //--------------------------------------------------------------------------------------
+    Real TEMReceiver::GetReferenceTime (  ) {
+        return referenceTime;
+    }		// -----  end of method TEMReceiver::GetReferenceTime  -----
+
+
+#ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  Serialize
+    //--------------------------------------------------------------------------------------
+    YAML::Node  TEMReceiver::Serialize (  ) const {
+        YAML::Node node = ReceiverPoints::Serialize();
+        node.SetTag( this->Name );
+        node["moment"] = moment;
+        node["referenceTime"] = referenceTime;
+        node["component"] = enum2String(component);
+
+        node["windowCentres"] = windowCentres;
+        node["windowWidths"] = windowWidths;
+        node["noiseSTD"] = noiseSTD;
+        //node["location"] = location;
+        return node;
+    }		// -----  end of method TEMReceiver::Serialize  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMReceiver
+    //      Method:  DeSerialize
+    //--------------------------------------------------------------------------------------
+    TEMReceiver* TEMReceiver::DeSerialize ( const YAML::Node& node  ) {
+        TEMReceiver* Object = new TEMReceiver(node);
+        Object->AttachTo(Object);
+        DESERIALIZECHECK( node, Object )
+        return Object ;
+
+    }		// -----  end of method TEMReceiver::DeSerialize  -----
+#endif
+
+}		// -----  end of Lemma  name  -----
+

Modules/TEM1D/src/TEMSurvey.cpp

@@ -0,0 +1,202 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      10/08/2014 01:52:04 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#include	"TEMSurvey.h"
+
+namespace Lemma {
+
+
+    // ====================  FRIEND METHODS  =====================
+
+    #ifdef HAVE_YAMLCPP
+    std::ostream &operator << (std::ostream &stream, const TEMSurvey &ob) {
+        stream << ob.Serialize()  << "\n---\n"; // End of doc --- a direct stream should encapulste object
+        return stream;
+    }
+    #else
+    std::ostream &operator<<(std::ostream &stream, const TEMSurvey &ob) {
+        stream << *(LemmaObject*)(&ob);
+        return stream;
+    }
+    #endif
+
+    // ====================  LIFECYCLE     =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurvey
+    //      Method:  TEMSurvey
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMSurvey::TEMSurvey (const std::string& name) : LemmaObject(name) {
+
+    }  // -----  end of method TEMSurvey::TEMSurvey  (constructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurvey
+    //      Method:  TEMSurvey
+    // Description:  DeSerializing constructor (protected)
+    //--------------------------------------------------------------------------------------
+    #ifdef HAVE_YAMLCPP
+    TEMSurvey::TEMSurvey (const YAML::Node& node) : LemmaObject(node) {
+
+        Lines.resize( node["numberOfLines"].as<int>( ) );
+
+    }  // -----  end of method TEMSurvey::TEMSurvey  (constructor)  -----
+    #endif
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurvey
+    //      Method:  New()
+    // Description:  public constructor
+    //--------------------------------------------------------------------------------------
+    TEMSurvey* TEMSurvey::New() {
+        TEMSurvey*  Obj = new TEMSurvey("TEMSurvey");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurvey
+    //      Method:  ~TEMSurvey
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMSurvey::~TEMSurvey () {
+
+    }  // -----  end of method TEMSurvey::~TEMSurvey  (destructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurvey
+    //      Method:  Delete
+    // Description:  public destructor
+    //--------------------------------------------------------------------------------------
+    void TEMSurvey::Delete() {
+        this->DetachFrom(this);
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurvey
+    //      Method:  Release
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    void TEMSurvey::Release() {
+        for (std::vector<TEMSurveyLine*>::iterator it = Lines.begin() ; it != Lines.end(); ++it) {
+            (*it)->DetachFrom(this);
+        }
+        delete this;
+    }
+
+    #ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurvey
+    //      Method:  Serialize
+    //--------------------------------------------------------------------------------------
+    YAML::Node  TEMSurvey::Serialize (  ) const {
+        YAML::Node node;
+        node.SetTag( this->Name );
+        node["numberOfLines"] = Lines.size();
+        for (unsigned int it = 0; it< Lines.size();  ++it) {
+            node[std::string("line_") +  to_string(it)] = Lines[it]->Serialize();
+        }
+        return node;
+    }		// -----  end of method TEMSurvey::Serialize  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurvey
+    //      Method:  DeSerialize
+    //--------------------------------------------------------------------------------------
+    TEMSurvey* TEMSurvey::DeSerialize ( const YAML::Node& node  ) {
+        TEMSurvey* Object = new TEMSurvey(node);
+        Object->AttachTo(Object);
+        DESERIALIZECHECK( node, Object )
+        return Object ;
+    }		// -----  end of method TEMSurvey::DeSerialize  -----
+    #endif
+
+
+
+        // ====================  OPERATORS    =======================
+
+    TEMSurveyLine* TEMSurvey::operator( ) ( const int& idx ) const {
+        return this->Lines[ idx ];
+    }
+
+    TEMSurveyLineRecord* TEMSurvey::operator( ) ( const int& iline, const int& irec ) const {
+        return Lines[ iline ]->GetRecord( irec );
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurvey
+    //      Method:  SetNumberOfLines
+    //--------------------------------------------------------------------------------------
+    void TEMSurvey::SetNumberOfLines ( const int& nlines  ) {
+
+        // clean up any old lines
+        for (std::vector<TEMSurveyLine*>::iterator it = Lines.begin() ; it != Lines.end(); ++it) {
+            (*it)->DetachFrom(this);
+        }
+        Lines.clear();
+
+        // Allocate these lines
+        Lines.reserve(nlines);
+        for (int il=0; il<nlines; ++il) {
+            Lines.push_back( new TEMSurveyLine("TEMSurveyLine") );
+            Lines[il]->AttachTo(this);
+        }
+
+        return ;
+    }		// -----  end of method TEMSurvey::SetNumberOfLines  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurvey
+    //      Method:  GetLine
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLine* TEMSurvey::GetLine ( const unsigned int&  iline ) {
+        return Lines[iline];
+    }		// -----  end of method TEMSurvey::GetLine  -----
+
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurvey
+    //      Method:  ForwardModel
+    //--------------------------------------------------------------------------------------
+    TEMSurveyData* TEMSurvey::ForwardModel ( LayeredEarthEM* model, bool additiveNoise ) {
+
+        TEMSurveyData* ForwardData = TEMSurveyData::New();
+            //ForwardData->SetNumberOfLines(Lines.size());
+
+        for (std::vector<TEMSurveyLine*>::iterator it = Lines.begin() ; it != Lines.end(); ++it) {
+
+            TEMSurveyLineData* LineData = ((*it)->ForwardModel( model, additiveNoise ) );
+            LineData->AttachTo(ForwardData);
+            ForwardData->LineData.push_back( LineData );
+        }
+
+        //for (int it=0; it<Lines.size(); ++it) {
+        //    Lines[it]->ForwardModel( model );
+        //}
+
+        return  ForwardData;
+    }		// -----  end of method TEMSurvey::ForwardModel  -----
+
+
+}		// -----  end of Lemma  name  -----
+

Modules/TEM1D/src/TEMSurveyData.cpp

@@ -0,0 +1,244 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      03/03/2015 10:00:22
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2015, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2015, Trevor Irons
+ */
+
+#include "TEMSurveyData.h"
+
+namespace Lemma {
+
+// ====================  FRIEND METHODS  =====================
+#ifdef HAVE_YAMLCPP
+std::ostream &operator << (std::ostream &stream, const TEMSurveyData &ob) {
+    stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
+    return stream;
+}
+#else
+std::ostream &operator<<(std::ostream &stream, const TEMSurveyData& ob) {
+    stream << *(LemmaObject*)(&ob);
+    return stream;
+}
+#endif
+
+// =================== OPERATORS ===============================
+
+TEMSurveyData* TEMSurveyData::operator + (const TEMSurveyData& d) {
+    TEMSurveyData* clone = Clone();
+    *clone += d;
+    return clone;
+}
+
+void TEMSurveyData::operator += (const TEMSurveyData& rhs) {
+
+    if ( this->GetNumberOfLines() != rhs.GetNumberOfLines() ) {
+        throw std::runtime_error( "Line mismatch in TEMSurveyData +=" );
+    }
+
+    for (int iline=0; iline<this->GetNumberOfLines(); ++iline ) {
+        *(*this)(iline) += *rhs(iline);
+        //*LineData[iline] += *rhs(iline);
+        //*LineData[iline] += *rhs.GetLine(iline);
+    }
+}
+
+void TEMSurveyData::operator -= (const TEMSurveyData& rhs) {
+
+    if ( this->GetNumberOfLines() != rhs.GetNumberOfLines() ) {
+        throw std::runtime_error( "Line mismatch in TEMSurveyData +=" );
+    }
+
+    for (int iline=0; iline<this->GetNumberOfLines(); ++iline ) {
+        *(*this)(iline) -= *rhs(iline);
+        //*LineData[iline] -= *rhs(iline);
+        //*LineData[iline] -= *rhs.GetLine(iline);
+    }
+
+}
+
+TEMSurveyData* TEMSurveyData::operator - (const TEMSurveyData& d) {
+    TEMSurveyData* clone = Clone();
+    *clone -= d;
+    return clone;
+}
+
+TEMSurveyLineData* TEMSurveyData::operator( ) ( const int& idx ) const {
+    return LineData[ idx ];
+}
+
+TEMSurveyLineRecordData* TEMSurveyData::operator( ) ( const int& iline, const int& irec ) const {
+    return LineData[ iline ]->GetRecord( irec );
+}
+
+// ====================  LIFECYCLE     =======================
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMSurveyData
+//      Method:  TEMSurveyData
+// Description:  constructor (protected)
+//--------------------------------------------------------------------------------------
+TEMSurveyData::TEMSurveyData (const std::string& name) : LemmaObject(name) {
+
+}  // -----  end of method TEMSurveyData::TEMSurveyData  (constructor)  -----
+
+#ifdef HAVE_YAMLCPP
+//--------------------------------------------------------------------------------------
+//       Class:  TEMSurveyData
+//      Method:  TEMSurveyData
+// Description:  DeSerializing constructor (protected)
+//--------------------------------------------------------------------------------------
+TEMSurveyData::TEMSurveyData (const YAML::Node& node) : LemmaObject(node) {
+
+    //SetNumberOfLines( node["numberOfLines"].as<int>( ) );
+
+    for (int ii=0; ii< node["numberOfLines"].as<int>( ); ++ii) {
+        //LineData.push_back( new TEMSurveyLineData("TEMSurveyLineData") );
+        LineData.push_back( TEMSurveyLineData::DeSerialize( node[ std::string("line_")  + to_string(ii)] ) );
+        LineData[ii]->AttachTo(this);
+    }
+
+
+}  // -----  end of method TEMSurveyData::TEMSurveyData  (constructor)  -----
+#endif
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMSurveyData
+//      Method:  New()
+// Description:  public constructor
+//--------------------------------------------------------------------------------------
+TEMSurveyData* TEMSurveyData::New() {
+    TEMSurveyData*  Obj = new TEMSurveyData("TEMSurveyData");
+    Obj->AttachTo(Obj);
+    return Obj;
+}
+
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMSurveyData
+//      Method:  Clone
+//--------------------------------------------------------------------------------------
+TEMSurveyData* TEMSurveyData::Clone (  ) {
+    return TEMSurveyData::DeSerialize( this->Serialize() ) ;
+}		// -----  end of method TEMSurveyData::Clone  -----
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMSurveyData
+//      Method:  ~TEMSurveyData
+// Description:  destructor (protected)
+//--------------------------------------------------------------------------------------
+TEMSurveyData::~TEMSurveyData () {
+
+}  // -----  end of method TEMSurveyData::~TEMSurveyData  (destructor)  -----
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMSurveyData
+//      Method:  Delete
+// Description:  public destructor
+//--------------------------------------------------------------------------------------
+void TEMSurveyData::Delete() {
+    this->DetachFrom(this);
+}
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMSurveyData
+//      Method:  Release
+// Description:  destructor (protected)
+//--------------------------------------------------------------------------------------
+void TEMSurveyData::Release() {
+
+    // clean up any old lines
+    for (std::vector<TEMSurveyLineData*>::iterator it = LineData.begin() ; it != LineData.end(); ++it) {
+        (*it)->DetachFrom(this);
+        (*it)->Delete();
+    }
+
+    delete this;
+}
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMSurveyData
+//      Method:  SetNumberOfLines
+//--------------------------------------------------------------------------------------
+void TEMSurveyData::SetNumberOfLines ( const int& nlines ) {
+
+        // clean up any old lines
+        for (std::vector<TEMSurveyLineData*>::iterator it = LineData.begin() ; it != LineData.end(); ++it) {
+            (*it)->DetachFrom(this);
+        }
+        LineData.clear();
+
+        // Allocate these lines
+        LineData.reserve(nlines);
+        for (int il=0; il<nlines; ++il) {
+            LineData.push_back( TEMSurveyLineData::New() );
+            LineData[il]->AttachTo(this);
+        }
+
+    return ;
+}		// -----  end of method TEMSurveyData::SetNumberOfLines  -----
+
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMSurveyData
+//      Method:  GetLine
+//--------------------------------------------------------------------------------------
+TEMSurveyLineData* TEMSurveyData::GetLine ( const int& iline) const {
+    return LineData[iline] ;
+}		// -----  end of method TEMSurveyData::GetLine  -----
+
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMSurveyData
+//      Method:  GetNumberOfLines
+//--------------------------------------------------------------------------------------
+int TEMSurveyData::GetNumberOfLines (  ) const {
+    return  LineData.size() ;
+}		// -----  end of method TEMSurveyData::GetNumberOfLines  -----
+
+
+
+#ifdef HAVE_YAMLCPP
+//--------------------------------------------------------------------------------------
+//       Class:  TEMSurveyData
+//      Method:  Serialize
+//--------------------------------------------------------------------------------------
+YAML::Node  TEMSurveyData::Serialize (  ) const {
+    YAML::Node node = LemmaObject::Serialize();;
+    node.SetTag( this->Name );
+    node["numberOfLines"] = LineData.size();
+
+    for (unsigned int it = 0; it<LineData.size();  ++it) {
+        node[std::string("line_") +  to_string(it)] = LineData[it]->Serialize();
+    }
+
+    return node;
+}		// -----  end of method TEMSurveyData::Serialize  -----
+
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMSurveyData
+//      Method:  DeSerialize
+//--------------------------------------------------------------------------------------
+TEMSurveyData* TEMSurveyData::DeSerialize ( const YAML::Node& node  ) {
+    TEMSurveyData* Object = new TEMSurveyData(node);
+    Object->AttachTo(Object);
+    DESERIALIZECHECK( node, Object )
+    return Object ;
+}		// -----  end of method TEMSurveyData::DeSerialize  -----
+#endif
+
+}		// -----  end of Lemma  name  -----
+

Modules/TEM1D/src/TEMSurveyLine.cpp

@@ -0,0 +1,162 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      10/10/2014 11:19:38 AM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#include "TEMSurveyLine.h"
+
+namespace Lemma {
+
+    // ====================  FRIEND METHODS  =====================
+#ifdef HAVE_YAMLCPP
+    std::ostream &operator << (std::ostream &stream, const TEMSurveyLine &ob) {
+        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
+        return stream;
+    }
+#else
+    std::ostream &operator<<(std::ostream &stream, const TEMSurveyLine& ob) {
+        stream << *(LemmaObject*)(&ob);
+        return stream;
+    }
+#endif
+
+    // ====================  LIFECYCLE     =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLine
+    //      Method:  TEMSurveyLine
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLine::TEMSurveyLine (const std::string& name) : LemmaObject(name) {
+
+    }  // -----  end of method TEMSurveyLine::TEMSurveyLine  (constructor)  -----
+
+#ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLine
+    //      Method:  TEMSurveyLine
+    // Description:  DeSerializing constructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLine::TEMSurveyLine (const YAML::Node& node) : LemmaObject(node) {
+
+    }  // -----  end of method TEMSurveyLine::TEMSurveyLine  (constructor)  -----
+#endif
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLine
+    //      Method:  ~TEMSurveyLine
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLine::~TEMSurveyLine () {
+
+    }  // -----  end of method TEMSurveyLine::~TEMSurveyLine  (destructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLine
+    //      Method:  Delete
+    // Description:  public destructor
+    //--------------------------------------------------------------------------------------
+    void TEMSurveyLine::Delete() {
+        // THIS is a private member, this class must be used through a TEMSurvey
+        this->DetachFrom(this);
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLine
+    //      Method:  Release
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    void TEMSurveyLine::Release() {
+        for (std::vector<TEMSurveyLineRecord*>::iterator it = Records.begin() ; it != Records.end(); ++it) {
+            (*it)->DetachFrom(this);
+        }
+        delete this;
+    }
+
+
+#ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLine
+    //      Method:  Serialize
+    //--------------------------------------------------------------------------------------
+    YAML::Node  TEMSurveyLine::Serialize (  ) const {
+        YAML::Node node;
+        node.SetTag( this->Name );
+        node["numberOfRecords"] = Records.size();
+        for (unsigned int it = 0; it< Records.size();  ++it) {
+            node[std::string("record_") +  to_string(it)] = Records[it]->Serialize();
+        }
+        return node;
+    }		// -----  end of method TEMSurveyLine::Serialize  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLine
+    //      Method:  DeSerialize
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLine* TEMSurveyLine::DeSerialize ( const YAML::Node& node  ) {
+        TEMSurveyLine* Object = new TEMSurveyLine(node);
+        Object->AttachTo(Object);
+        DESERIALIZECHECK( node, Object )
+            return Object ;
+    }		// -----  end of method TEMSurveyLine::DeSerialize  -----
+#endif
+
+    TEMSurveyLineRecord* TEMSurveyLine::GetRecord( const unsigned int& irec )  {
+        return Records[irec];
+    }
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLine
+    //      Method:  SetNumberOfRecords
+    //--------------------------------------------------------------------------------------
+    void TEMSurveyLine::SetNumberOfRecords ( const int& nrec  ) {
+
+        // clean up any old records
+        for (std::vector<TEMSurveyLineRecord*>::iterator it = Records.begin() ; it != Records.end(); ++it) {
+            (*it)->DetachFrom(this);
+        }
+        Records.clear();
+
+        // Allocate these lines
+        Records.reserve(nrec);
+        for (int ir=0; ir<nrec; ++ir) {
+            Records.push_back( new TEMSurveyLineRecord("TEMSurveyLineRecord") );
+            Records[ir]->AttachTo(this);
+        }
+
+        return ;
+    }		// -----  end of method TEMSurveyLine::SetNumberOfRecords  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLine
+    //      Method:  ForwardModel
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineData* TEMSurveyLine::ForwardModel ( LayeredEarthEM* Model, bool additiveNoise ) {
+        TEMSurveyLineData* Data = TEMSurveyLineData::New();
+        for (std::vector<TEMSurveyLineRecord*>::iterator it = Records.begin() ; it != Records.end(); ++it) {
+            TEMSurveyLineRecordData* RecData = (*it)->ForwardModel(Model, additiveNoise) ;
+            RecData->AttachTo(Data);
+            Data->RecordData.push_back( RecData );
+        }
+        return Data;
+    }		// -----  end of method TEMSurveyLine::ForwardModel  -----
+
+
+}		// -----  end of Lemma  name  -----

Modules/TEM1D/src/TEMSurveyLineData.cpp

@@ -0,0 +1,230 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      03/03/2015 10:23:22
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2015, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2015, Trevor Irons
+ */
+
+#include "TEMSurveyLineData.h"
+
+namespace Lemma {
+
+    // ====================  FRIEND METHODS  =====================
+#ifdef HAVE_YAMLCPP
+    std::ostream &operator << (std::ostream &stream, const TEMSurveyLineData &ob) {
+        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
+        return stream;
+    }
+#else
+    std::ostream &operator<<(std::ostream &stream, const TEMSurveyLineData& ob) {
+        stream << *(LemmaObject*)(&ob);
+        return stream;
+    }
+#endif
+
+    // ====================  LIFECYCLE     =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineData
+    //      Method:  TEMSurveyLineData
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineData::TEMSurveyLineData (const std::string& name) : LemmaObject(name) {
+
+    }  // -----  end of method TEMSurveyLineData::TEMSurveyLineData  (constructor)  -----
+
+#ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineData
+    //      Method:  TEMSurveyLineData
+    // Description:  DeSerializing constructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineData::TEMSurveyLineData (const YAML::Node& node) : LemmaObject(node) {
+        for (int ii=0; ii< node["numberOfRecords"].as<int>( ); ++ii) {
+            RecordData.push_back( TEMSurveyLineRecordData::DeSerialize( node[ std::string("record_")  + to_string(ii)] ) );
+            RecordData[ii]->AttachTo(this);
+        }
+    }  // -----  end of method TEMSurveyLineData::TEMSurveyLineData  (constructor)  -----
+#endif
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineData
+    //      Method:  New()
+    // Description:  public constructor
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineData* TEMSurveyLineData::New() {
+        TEMSurveyLineData*  Obj = new TEMSurveyLineData("TEMSurveyLineData");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecordData
+    //      Method:  Clone
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineData* TEMSurveyLineData::Clone (  ) {
+        return TEMSurveyLineData::DeSerialize( this->Serialize() )  ;
+    }		// -----  end of method TEMSurveyLineRecordData::Clone  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineData
+    //      Method:  ~TEMSurveyLineData
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineData::~TEMSurveyLineData () {
+
+    }  // -----  end of method TEMSurveyLineData::~TEMSurveyLineData  (destructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineData
+    //      Method:  Delete
+    // Description:  public destructor
+    //--------------------------------------------------------------------------------------
+    void TEMSurveyLineData::Delete() {
+        this->DetachFrom(this);
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineData
+    //      Method:  Release
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    void TEMSurveyLineData::Release() {
+        for (std::vector<TEMSurveyLineRecordData*>::iterator it = RecordData.begin() ; it != RecordData.end(); ++it) {
+            (*it)->DetachFrom(this);
+            (*it)->Delete();
+        }
+        delete this;
+    }
+
+    // =================== OPERATORS ===============================
+
+    TEMSurveyLineRecordData* TEMSurveyLineData::operator( ) ( const int& idx ) const {
+        return RecordData[ idx ];
+    }
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineData
+    //      Method:  operator +=
+    //--------------------------------------------------------------------------------------
+    void TEMSurveyLineData::operator += ( const TEMSurveyLineData& rhs) {
+
+        if ( this->GetNumberOfRecords() != rhs.GetNumberOfRecords() ) {
+            throw std::runtime_error( "Record mismatch in TEMSurveyLineData +=" );
+        }
+
+        for (int irec=0; irec<this->GetNumberOfRecords(); ++irec ) {
+            *(*this)(irec) += *rhs(irec);
+            //*LineData[irec] += *rhs(irec);
+            //*LineData[irec] += *rhs.GetLine(irec);
+        }
+
+        return ;
+    }		// -----  end of method TEMSurveyLineData::+=  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineData
+    //      Method:  operator +
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineData* TEMSurveyLineData::operator + ( const TEMSurveyLineData& rhs) {
+        TEMSurveyLineData* clone = Clone();
+        *clone += rhs;
+        return clone;
+    }		// -----  end of method TEMSurveyLineData::operator +  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineData
+    //      Method:  operator -=
+    //--------------------------------------------------------------------------------------
+    void TEMSurveyLineData::operator -= ( const TEMSurveyLineData& rhs ) {
+
+        if ( this->GetNumberOfRecords() != rhs.GetNumberOfRecords() ) {
+            throw std::runtime_error( "Record mismatch in TEMSurveyLineData +=" );
+        }
+
+        for (int irec=0; irec<this->GetNumberOfRecords(); ++irec ) {
+            *(*this)(irec) -= *rhs(irec);
+            //*LineData[irec] -= *rhs(irec);
+            //*LineData[irec] -= *rhs.GetLine(irec);
+        }
+        return ;
+    }		// -----  end of method TEMSurveyLineData::operator -=  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineData
+    //      Method:  operator -
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineData* TEMSurveyLineData::operator - ( const TEMSurveyLineData& rhs) {
+        TEMSurveyLineData* clone = Clone();
+        *clone -= rhs;
+        return clone;
+    }		// -----  end of method TEMSurveyLineData::operator -  -----
+
+
+    // ====================  ACCESS        =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineData
+    //      Method:  GetRecord
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineRecordData*    TEMSurveyLineData::GetRecord(const int& ir) const {
+        return RecordData[ir];
+    }		// -----  end of method TEMSurveyLineData::GetRecord  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecordData
+    //      Method:  GetNumberOfRecords
+    //--------------------------------------------------------------------------------------
+    int TEMSurveyLineData::GetNumberOfRecords (  ) const {
+        return RecordData.size();
+    }		// -----  end of method TEMSurveyLineRecordData::GetNumberOfRecords  -----
+
+
+#ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineData
+    //      Method:  Serialize
+    //--------------------------------------------------------------------------------------
+    YAML::Node  TEMSurveyLineData::Serialize (  ) const {
+        YAML::Node node = LemmaObject::Serialize();;
+        node.SetTag( this->Name );
+        node["numberOfRecords"] = RecordData.size();
+        // FILL IN CLASS SPECIFICS HERE
+        for (unsigned int it = 0; it< RecordData.size();  ++it) {
+            node[std::string("record_") +  to_string(it)] = RecordData[it]->Serialize();
+        }
+        return node;
+    }		// -----  end of method TEMSurveyLineData::Serialize  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineData
+    //      Method:  DeSerialize
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineData* TEMSurveyLineData::DeSerialize ( const YAML::Node& node  ) {
+        TEMSurveyLineData* Object = new TEMSurveyLineData(node);
+        Object->AttachTo(Object);
+        DESERIALIZECHECK( node, Object )
+            return Object ;
+    }		// -----  end of method TEMSurveyLineData::DeSerialize  -----
+#endif
+
+}		// -----  end of Lemma  name  -----
+

Modules/TEM1D/src/TEMSurveyLineRecord.cpp

@@ -0,0 +1,254 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      10/10/2014 12:23:07 PM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#include "TEMSurveyLineRecord.h"
+
+namespace Lemma {
+
+
+    // ====================  FRIEND METHODS  =====================
+#ifdef HAVE_YAMLCPP
+    std::ostream &operator << (std::ostream &stream, const TEMSurveyLineRecord &ob) {
+        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
+        return stream;
+    }
+#else
+    std::ostream &operator<<(std::ostream &stream, const TEMSurveyLineRecord& ob) {
+        stream << *(LemmaObject*)(&ob);
+        return stream;
+    }
+#endif
+
+    // ====================  LIFECYCLE     =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecord
+    //      Method:  TEMSurveyLineRecord
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineRecord::TEMSurveyLineRecord (const std::string& name) : LemmaObject(name),
+        numberOfPulseSequences(0)
+    {
+
+    }  // -----  end of method TEMSurveyLineRecord::TEMSurveyLineRecord  (constructor)  -----
+
+#ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecord
+    //      Method:  TEMSurveyLineRecord
+    // Description:  DeSerializing constructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineRecord::TEMSurveyLineRecord (const YAML::Node& node) : LemmaObject(node),
+        numberOfPulseSequences(0)
+    {
+
+    }  // -----  end of method TEMSurveyLineRecord::TEMSurveyLineRecord  (constructor)  -----
+#endif
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecord
+    //      Method:  ~TEMSurveyLineRecord
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineRecord::~TEMSurveyLineRecord () {
+
+        for (unsigned int ip=0; ip<Transmitters.size(); ++ip) {
+            if (Transmitters[ip] != NULL) {
+                Transmitters[ip]->DetachFrom(this);
+            }
+        }
+        for (unsigned int ir=0; ir<Receivers.size(); ++ir) {
+            if (Receivers[ir] != NULL) {
+                Receivers[ir]->DetachFrom(this);
+            }
+        }
+
+    }  // -----  end of method TEMSurveyLineRecord::~TEMSurveyLineRecord  (destructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecord
+    //      Method:  Delete
+    // Description:  public destructor
+    //--------------------------------------------------------------------------------------
+    void TEMSurveyLineRecord::Delete() {
+        this->DetachFrom(this);
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecord
+    //      Method:  Release
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    void TEMSurveyLineRecord::Release() {
+        delete this;
+    }
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecord
+    //      Method:  SetPulseSequenceReceiverPair
+    //--------------------------------------------------------------------------------------
+    void TEMSurveyLineRecord::SetTransmitterReceiverPair ( const int& ii, TEMTransmitter* Tx, TEMReceiver* Rx  ) {
+        Receivers[ii] = Rx;
+        Rx->AttachTo(this);
+
+        Transmitters[ii] = Tx;
+        Tx->AttachTo(this);
+        return ;
+    }		// -----  end of method TEMSurveyLineRecord::SetPulseSequenceReceiverPair  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecord
+    //      Method:  GetReceiver
+    //--------------------------------------------------------------------------------------
+    TEMReceiver* TEMSurveyLineRecord::GetReceiver ( const int& irec  ) {
+        if ( irec >= (int)(Receivers.size()) ) {
+            throw std::runtime_error( "TEMSurveyLineRecord::GetReceiver(const int& irec)--array bounds error" );
+        }
+        return Receivers[irec] ;
+    }		// -----  end of method TEMSurveyLineRecord::GetReceiver  -----
+
+
+#ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecord
+    //      Method:  Serialize
+    //--------------------------------------------------------------------------------------
+    YAML::Node  TEMSurveyLineRecord::Serialize (  ) const {
+        YAML::Node node;
+        node.SetTag( this->Name );
+        node["numberOfPulseSequences"] = numberOfPulseSequences;
+
+        // FILL IN CLASS SPECIFICS HERE
+
+        for( int is=0; is<numberOfPulseSequences; ++is) {
+            node[std::string("pulse_") + to_string(is)]    = Transmitters[is]->Serialize();
+            node[std::string("receiver_") + to_string(is)] = Receivers[is]->Serialize();
+        }
+
+
+        return node;
+    }		// -----  end of method TEMSurveyLineRecord::Serialize  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecord
+    //      Method:  DeSerialize
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineRecord* TEMSurveyLineRecord::DeSerialize ( const YAML::Node& node  ) {
+        TEMSurveyLineRecord* Object = new TEMSurveyLineRecord(node);
+        Object->AttachTo(Object);
+        DESERIALIZECHECK( node, Object )
+            return Object ;
+    }		// -----  end of method TEMSurveyLineRecord::DeSerialize  -----
+#endif
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecord
+    //      Method:  SetNumberOfPulseSequences
+    //--------------------------------------------------------------------------------------
+    void TEMSurveyLineRecord::SetNumberOfPulseSequences ( const int& nseq ) {
+
+        for (unsigned int ip=0; ip<Transmitters.size(); ++ip) {
+            Transmitters[ip]->DetachFrom(this);
+        }
+        for (unsigned int ir=0; ir<Receivers.size(); ++ir) {
+            Receivers[ir]->DetachFrom(this);
+        }
+        Transmitters.clear();
+        Receivers.clear();
+
+        numberOfPulseSequences = nseq;
+
+        Receivers.reserve(nseq);
+        Transmitters.reserve(nseq);
+        for (int ir=0; ir<nseq; ++ir) {
+            Transmitters.push_back( NULL );
+            Receivers.push_back( NULL );
+        }
+
+        return ;
+    }		// -----  end of method TEMSurveyLineRecord::SetNumberOfPulseSequences  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecord
+    //      Method:  GetNumberOfPulseSequences
+    //--------------------------------------------------------------------------------------
+    int TEMSurveyLineRecord::GetNumberOfPulseSequences (  ) {
+        return numberOfPulseSequences ;
+    }		// -----  end of method TEMSurveyLineRecord::GetNumberOfPulseSequences  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecord
+    //      Method:  ForwardModel
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineRecordData* TEMSurveyLineRecord::ForwardModel ( LayeredEarthEM* model, bool additiveNoise ) {
+
+        TEMSurveyLineRecordData* Data = TEMSurveyLineRecordData::New();
+
+        // DO I want to work with InstrumentTem here? Or just roll it myself at this point?
+        for (unsigned int ip=0; ip<Transmitters.size(); ++ip) {
+
+            InstrumentTem *instrument = InstrumentTem::New();
+
+            // For thread safety...
+            TEMTransmitter*  TC =  Transmitters[ip]->Clone();
+            TEMReceiver* RC = Receivers[ip]->Clone();
+
+            // TODO some of this needs to be moved logic checked or use overriden functions, etc.
+            instrument->EMEarthModel(model);
+	        instrument->SetTransmitLoop( TC );
+            instrument->SetReferenceTime( RC->GetReferenceTime() );
+	        instrument->SetTimeGates( RC->GetWindowCentres(), RC->GetWindowWidths() );
+	        instrument->SetReceiver( RC );   // Clone??
+            instrument->SetReceiverType(INDUCTIVE);
+            instrument->SetPulse( TC->GetWfmAmps(), TC->GetWfmTimes() );
+
+            // TODO pass this
+            //instrument->MakeLaggedCalculation( FHTKEY51 );
+            instrument->MakeLaggedCalculation( ANDERSON801 );
+
+            Data->DataSeries.push_back( MU0*instrument->GetMeasurements().col(1) );
+            Data->GateCentres.push_back( RC->GetWindowCentres() );
+
+            if (additiveNoise) {
+                Data->DataSeries.back() += RC->SampleNoise();
+            }
+
+//                 int nlag = instrument->GetMeasurements().rows();
+//                 std::cout.precision(12);
+//                 std::cout << "// time [s]  dB/dt [T/s] \n";
+//                 for (int ii=0; ii<nlag; ii++) {
+//  		            std::cout<<"  "<<instrument->GetMeasurements()(ii,0)<<"  "<< MU0*instrument->GetMeasurements()(ii,1)<<std::endl;
+//  	            }
+
+            instrument->Delete();
+            TC->Delete();
+            RC->Delete();
+        }
+
+        return Data;
+    }		// -----  end of method TEMSurveyLineRecord::ForwardModel  -----
+
+
+}		// -----  end of Lemma  name  -----

Modules/TEM1D/src/TEMSurveyLineRecordData.cpp

@@ -0,0 +1,248 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      03/03/2015 10:34:56
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2015, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2015, Trevor Irons
+ */
+
+#include "TEMSurveyLineRecordData.h"
+
+namespace Lemma {
+
+
+    // ====================  FRIEND METHODS  =====================
+#ifdef HAVE_YAMLCPP
+    std::ostream &operator << (std::ostream &stream, const TEMSurveyLineRecordData &ob) {
+        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
+        return stream;
+    }
+#else
+    std::ostream &operator<<(std::ostream &stream, const TEMSurveyLineRecordData& ob) {
+        stream << *(LemmaObject*)(&ob);
+        return stream;
+    }
+#endif
+
+    // ====================  LIFECYCLE     =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecordData
+    //      Method:  TEMSurveyLineRecordData
+    // Description:  constructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineRecordData::TEMSurveyLineRecordData (const std::string& name) : LemmaObject(name) {
+
+    }  // -----  end of method TEMSurveyLineRecordData::TEMSurveyLineRecordData  (constructor)  -----
+
+#ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecordData
+    //      Method:  TEMSurveyLineRecordData
+    // Description:  DeSerializing constructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineRecordData::TEMSurveyLineRecordData (const YAML::Node& node) : LemmaObject(node) {
+        for (int ii=0; ii< node["numberOfSeries"].as<int>( ); ++ii) {
+            DataSeries.push_back( node["DataSeries_" + to_string(ii)].as<VectorXr>() );
+            GateCentres.push_back( node["GateCentres_" + to_string(ii)].as<VectorXr>() );
+        }
+    }  // -----  end of method TEMSurveyLineRecordData::TEMSurveyLineRecordData  (constructor)  -----
+#endif
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecordData
+    //      Method:  New()
+    // Description:  public constructor
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineRecordData* TEMSurveyLineRecordData::New() {
+        TEMSurveyLineRecordData*  Obj = new TEMSurveyLineRecordData("TEMSurveyLineRecordData");
+        Obj->AttachTo(Obj);
+        return Obj;
+    }
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecordData
+    //      Method:  Clone
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineRecordData* TEMSurveyLineRecordData::Clone (  ) {
+        return DeSerialize( this->Serialize() )  ;
+    }		// -----  end of method TEMSurveyLineRecordData::Clone  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecordData
+    //      Method:  ~TEMSurveyLineRecordData
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineRecordData::~TEMSurveyLineRecordData () {
+
+    }  // -----  end of method TEMSurveyLineRecordData::~TEMSurveyLineRecordData  (destructor)  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecordData
+    //      Method:  Delete
+    // Description:  public destructor
+    //--------------------------------------------------------------------------------------
+    void TEMSurveyLineRecordData::Delete() {
+        this->DetachFrom(this);
+    }
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecordData
+    //      Method:  Release
+    // Description:  destructor (protected)
+    //--------------------------------------------------------------------------------------
+    void TEMSurveyLineRecordData::Release() {
+        delete this;
+    }
+
+        // ====================  OPERATORS     =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecordData
+    //      Method:  operator +
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineRecordData* TEMSurveyLineRecordData::operator + ( const TEMSurveyLineRecordData& Survey ) {
+        TEMSurveyLineRecordData* clone = this->Clone();
+        for (unsigned int ir=0; ir<DataSeries.size(); ++ir) {
+            clone->DataSeries[ir] += Survey.DataSeries[ir];
+        }
+        return clone;
+    }		// -----  end of method TEMSurveyLineRecordData::operator +  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecordData
+    //      Method:  operator -
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineRecordData* TEMSurveyLineRecordData::operator - ( const TEMSurveyLineRecordData& Survey ) {
+        TEMSurveyLineRecordData* clone = this->Clone();
+        for (unsigned int ir=0; ir<DataSeries.size(); ++ir) {
+            clone->DataSeries[ir] -= Survey.DataSeries[ir];
+        }
+        return clone;
+    }		// -----  end of method TEMSurveyLineRecordData::operator -  -----
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecordData
+    //      Method:  operator +=
+    //--------------------------------------------------------------------------------------
+    void TEMSurveyLineRecordData::operator += ( const TEMSurveyLineRecordData& Survey ) {
+
+        if (DataSeries.size() != Survey.DataSeries.size()) {
+            throw std::runtime_error("size mismatch in TEMSurveyLineRecordData::operator +=");
+        }
+
+        for (unsigned int ii=0; ii<DataSeries.size(); ++ii) {
+            this->DataSeries[ii] += Survey.DataSeries[ii];
+        }
+
+        return ;
+    }		// -----  end of method TEMSurveyLineRecordData::operator +=  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecordData
+    //      Method:  operator -=
+    //--------------------------------------------------------------------------------------
+    void TEMSurveyLineRecordData::operator -= ( const TEMSurveyLineRecordData& Survey ) {
+
+        if (DataSeries.size() != Survey.DataSeries.size()) {
+            throw std::runtime_error("size mismatch in TEMSurveyLineRecordData::operator +=");
+        }
+
+        for (unsigned int ii=0; ii<DataSeries.size(); ++ii) {
+            this->DataSeries[ii] -= Survey.DataSeries[ii];
+        }
+
+        return ;
+    }		// -----  end of method TEMSurveyLineRecordData::operator -=  -----
+
+
+        // ====================  ACCESS        =======================
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecordData
+    //      Method:  GetCombinedData
+    //--------------------------------------------------------------------------------------
+    VectorXr TEMSurveyLineRecordData::GetCombinedData (  ) {
+
+        int nd = 0;
+        for (unsigned int id=0; id<DataSeries.size(); ++id) {
+            nd += DataSeries[id].size();
+        }
+        VectorXr combined = VectorXr(nd);
+
+        nd = 0;
+        for (unsigned int id=0; id<DataSeries.size(); ++id) {
+            combined.segment(nd, DataSeries[id].size()) = DataSeries[id];
+            nd += DataSeries[id].size();
+        }
+
+        return  combined;
+    }		// -----  end of method TEMSurveyLineRecordData::GetCombinedData  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecordData
+    //      Method:  GetCombinedGateCentres
+    //--------------------------------------------------------------------------------------
+    VectorXr TEMSurveyLineRecordData::GetCombinedGateCentres (  ) {
+        int nd = 0;
+        for (unsigned int id=0; id<GateCentres.size(); ++id) {
+            nd += GateCentres[id].size();
+        }
+        VectorXr combined = VectorXr(nd);
+
+        nd = 0;
+        for (unsigned int id=0; id<GateCentres.size(); ++id) {
+            combined.segment(nd, GateCentres[id].size()) = GateCentres[id];
+            nd += GateCentres[id].size();
+        }
+
+        return  combined;
+    }		// -----  end of method TEMSurveyLineRecordData::GetCombinedGateCentres  -----
+
+
+#ifdef HAVE_YAMLCPP
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecordData
+    //      Method:  Serialize
+    //--------------------------------------------------------------------------------------
+    YAML::Node  TEMSurveyLineRecordData::Serialize (  ) const {
+        YAML::Node node = LemmaObject::Serialize();;
+        node.SetTag( this->Name );
+        node["numberOfSeries"] = DataSeries.size();
+        for (unsigned int is=0; is<DataSeries.size(); ++is) {
+            node[std::string("DataSeries_") + to_string(is)] = DataSeries[is];
+            node[std::string("GateCentres_") + to_string(is)] = GateCentres[is];
+        }
+        return node;
+    }		// -----  end of method TEMSurveyLineRecordData::Serialize  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  TEMSurveyLineRecordData
+    //      Method:  DeSerialize
+    //--------------------------------------------------------------------------------------
+    TEMSurveyLineRecordData* TEMSurveyLineRecordData::DeSerialize ( const YAML::Node& node  ) {
+        TEMSurveyLineRecordData* Object = new TEMSurveyLineRecordData(node);
+        Object->AttachTo(Object);
+        DESERIALIZECHECK( node, Object )
+            return Object ;
+    }		// -----  end of method TEMSurveyLineRecordData::DeSerialize  -----
+#endif
+
+}		// -----  end of Lemma  name  -----
+

Modules/TEM1D/src/TEMTransmitter.cpp

@@ -0,0 +1,227 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API.
+ * More information is available at http://lemmasoftware.org
+ */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ */
+
+/**
+ * @file
+ * @date      09/29/2014 11:43:28 AM
+ * @version   $Id$
+ * @author    Trevor Irons (ti)
+ * @email     Trevor.Irons@xri-geo.com
+ * @copyright Copyright (c) 2014, XRI Geophysics, LLC
+ * @copyright Copyright (c) 2014, Trevor Irons
+ */
+
+#include "TEMTransmitter.h"
+
+namespace Lemma {
+
+// ====================  FRIEND METHODS  =====================
+
+#ifdef HAVE_YAMLCPP
+std::ostream &operator << (std::ostream &stream, const TEMTransmitter &ob) {
+    stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
+    return stream;
+}
+// TODO CONSIDER INPUT OPERATOR TOO!
+//std::ostream &operator << (std::ostream &stream, const TEMTransmitter &ob) {
+//    stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
+//    return stream;
+//}
+#else
+std::ostream &operator << (std::ostream &stream, const TEMTransmitter &ob) {
+    stream << *(PolygonalWireAntenna*)(&ob);
+    stream << "YOU SHOULD COMPILE WITH YAML-CPP\n";
+    return stream;
+}
+#endif
+
+
+// ====================  LIFECYCLE     =======================
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMTransmitter
+//      Method:  TEMTransmitter
+// Description:  constructor (protected)
+//--------------------------------------------------------------------------------------
+TEMTransmitter::TEMTransmitter (const std::string& name) : PolygonalWireAntenna(name),
+    repFreq(0), repFreqUnits(HZ) {
+
+}  // -----  end of method TEMTransmitter::TEMTransmitter  (constructor)  -----
+
+#ifdef HAVE_YAMLCPP
+//--------------------------------------------------------------------------------------
+//       Class:  TEMTransmitter
+//      Method:  TEMTransmitter
+// Description:  Deserializing constructor (protected)
+//--------------------------------------------------------------------------------------
+TEMTransmitter::TEMTransmitter (const YAML::Node& node) : PolygonalWireAntenna(node) {
+
+    repFreq =  node["repFreq"].as<Real>();
+    repFreqUnits =  string2Enum<FREQUENCYUNITS>( node["repFreqUnits"].as<std::string>() );
+    wfmTimes = node["wfmTimes"].as<VectorXr>();
+    wfmTimes = node["wfmAmps"].as<VectorXr>();
+
+}  // -----  end of method TEMTransmitter::TEMTransmitter  (constructor)  -----
+#endif
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMTransmitter
+//      Method:  New()
+// Description:  public constructor
+//--------------------------------------------------------------------------------------
+TEMTransmitter* TEMTransmitter::New() {
+    TEMTransmitter*  Obj = new TEMTransmitter("TEMTransmitter");
+    Obj->AttachTo(Obj);
+    return Obj;
+}
+
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMTransmitter
+//      Method:  Clone
+//--------------------------------------------------------------------------------------
+TEMTransmitter* TEMTransmitter::Clone (  ) {
+    TEMTransmitter* copy = TEMTransmitter::New();
+    //copy->AttachTo(copy); // NO! Attached above!
+	copy->NumberOfPoints = this->NumberOfPoints;
+	copy->Freqs = this->Freqs;
+	copy->Current = this->Current;
+	copy->NumberOfTurns = this->NumberOfTurns;
+	copy->Points = this->Points;
+	//copy->Dipoles = this->Dipoles; // no, disaster
+
+    copy->repFreq = this->repFreq;
+    copy->repFreqUnits = this->repFreqUnits;
+    copy->wfmTimes = this->wfmTimes;
+    copy->wfmAmps = this->wfmAmps;
+
+	return copy;
+}		// -----  end of method TEMTransmitter::Clone  -----
+
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMTransmitter
+//      Method:  ~TEMTransmitter
+// Description:  destructor (protected)
+//--------------------------------------------------------------------------------------
+TEMTransmitter::~TEMTransmitter () {
+
+}  // -----  end of method TEMTransmitter::~TEMTransmitter  (destructor)  -----
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMTransmitter
+//      Method:  Delete
+// Description:  public destructor
+//--------------------------------------------------------------------------------------
+void TEMTransmitter::Delete() {
+    this->DetachFrom(this);
+}
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMTransmitter
+//      Method:  Release
+// Description:  destructor (protected)
+//--------------------------------------------------------------------------------------
+void TEMTransmitter::Release() {
+    delete this;
+}
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMTransmitter
+//      Method:  Serialize
+//--------------------------------------------------------------------------------------
+#ifdef HAVE_YAMLCPP
+YAML::Node TEMTransmitter::Serialize (  ) const {
+
+    YAML::Node node = PolygonalWireAntenna::Serialize();
+        // or we could do just like below. Same basic uglyness
+        node.SetTag( this->Name) ; //((PolygonalWireAntenna*)(&ob))->GetName() );
+        //node["address"] =  ss.str();
+
+        node["repFreq"]      = this->repFreq;
+        node["repFreqUnits"] = enum2String(repFreqUnits);
+        node["wfmTimes"] = wfmTimes;
+        node["wfmAmps"] = wfmAmps;
+
+    return node;
+}		// -----  end of method TEMTransmitter::Serialize  -----
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMTransmitter
+//      Method:  DeSerialize
+//--------------------------------------------------------------------------------------
+TEMTransmitter* TEMTransmitter::DeSerialize ( const  YAML::Node& node  ) {
+    TEMTransmitter* Object = new TEMTransmitter(node);
+    Object->AttachTo(Object);
+    DESERIALIZECHECK( node, Object )
+    return  Object;
+}		// -----  end of method TEMTransmitter::DeSerialize  -----
+#endif
+
+    // ====================  INQUIRY       =======================
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMTransmitter
+//      Method:  SetRepFrequency
+//--------------------------------------------------------------------------------------
+void TEMTransmitter::SetRepFrequency ( const Real& fr, const FREQUENCYUNITS& units ) {
+    repFreq = fr;
+    repFreqUnits = units;
+    return ;
+}		// -----  end of method TEMTransmitter::SetRepFrequency  -----
+
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMTransmitter
+//      Method:  SetWaveform
+//--------------------------------------------------------------------------------------
+void TEMTransmitter::SetWaveform (  const VectorXr& times, const VectorXr& amps, const TIMEUNITS& units ) {
+    // switch units ?
+    switch (units) {
+        case SEC:
+            wfmTimes = times;
+            break;
+        case MILLISEC:
+            wfmTimes = times*1e-3 ;
+            break;
+        case MICROSEC:
+            wfmTimes = times*1e-6 ;
+            break;
+        case NANOSEC:
+            wfmTimes = times*1e-9 ;
+            break;
+        case PICOSEC:
+            wfmTimes = times*1e-12 ;
+            break;
+    };
+    wfmAmps = amps;
+    return ;
+}		// -----  end of method TEMTransmitter::SetWaveform  -----
+
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMTransmitter
+//      Method:  GetWfmAmps
+//--------------------------------------------------------------------------------------
+VectorXr TEMTransmitter::GetWfmAmps (  ) {
+    return wfmAmps;
+}		// -----  end of method TEMTransmitter::GetWfmAmps  -----
+
+
+
+//--------------------------------------------------------------------------------------
+//       Class:  TEMTransmitter
+//      Method:  GetWfmTimes
+//--------------------------------------------------------------------------------------
+VectorXr TEMTransmitter::GetWfmTimes (  ) {
+    return wfmTimes;
+}		// -----  end of method TEMTransmitter::GetWfmTimes  -----
+
+
+} // namespace Lemma

Modules/TEM1D/src/instrumenttem.cpp

@@ -0,0 +1,449 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   M. Andy Kass, Edited Trevor Irons 02/28/2014
+  @date     02/10/2011
+  @version  $Id: instrumenttem.cpp 266 2015-04-01 03:24:00Z tirons $
+ **/
+#include "instrumenttem.h"
+
+namespace Lemma {
+
+	std::ostream &operator<<(std::ostream &stream,
+		const InstrumentTem &ob) {
+	stream << *(LemmaObject*)(&ob);
+	return stream;
+	}
+
+	// =======================  Lifecycle  ==================================
+
+	InstrumentTem::InstrumentTem(const std::string &name) : Instrument(name),
+		Antenna(NULL), Receiver(NULL), EarthMod(NULL), Dipole(NULL), bipolarWaveform(true),
+        NPreviousPulse(0), RefTime(0.0), PulseT(.06), TxFreq(0.30), RType(INDUCTIVE) {
+	}
+
+	InstrumentTem::~InstrumentTem() {
+		if (NumberOfReferences != 0) {
+			throw DeleteObjectWithReferences(this);
+		}
+
+        if (this->Antenna != NULL) {
+			this->Antenna->DetachFrom(this);
+		}
+
+		if (this->Dipole != NULL) {
+			this->Dipole->DetachFrom(this);
+		}
+
+        if (this->EarthMod != NULL) {
+			this->EarthMod->DetachFrom(this);
+		}
+
+        if (this->Receiver != NULL) {
+			this->Receiver->DetachFrom(this);
+		}
+
+	}
+
+	InstrumentTem* InstrumentTem::New() {
+		InstrumentTem* Obj = new InstrumentTem("InstrumentTem");
+		Obj->AttachTo(Obj);
+		return Obj;
+	}
+
+	void InstrumentTem::Delete() {
+		this->DetachFrom(this);
+	}
+
+	void InstrumentTem::Release() {
+		delete this;
+	}
+
+	// =======================  Operations  =================================
+	void InstrumentTem::MakeDirectCalculation( const HANKELTRANSFORMTYPE& hType) {
+
+		//int temp;
+		int NumTimes;
+		Real answer;
+		EMEarth1D *EMEarthLocal=EMEarth1D::New();
+		EMEarthLocal->AttachLayeredEarthEM(this->EarthMod);
+
+		//DigitalFilterCosTrans *DFIntegrate=DigitalFilterCosTrans::New();
+		DigitalFilterSinTrans *DFIntegrate=DigitalFilterSinTrans::New();
+
+		TemIntegrationKernel *TEMIntKern=TemIntegrationKernel::New();
+		TEMIntKern->SetEMEarth1D(EMEarthLocal);
+		//TEMIntKern->SetTransmitter(this->Antenna);
+		TEMIntKern->SetReceiver(this->Receiver);
+		DFIntegrate->AttachKernel(TEMIntKern);
+
+		if (this->Dipole != NULL) {  //AND this->Antenna == NULL
+			EMEarthLocal->AttachDipoleSource(this->Dipole);
+			TEMIntKern->SetDipole(this->Dipole);
+		}
+		if (this->Antenna != NULL) { //AND this->Dipole == NULL
+			EMEarthLocal->AttachWireAntenna(this->Antenna);
+			TEMIntKern->SetTransmitter(this->Antenna);
+		}
+		EMEarthLocal->SetFieldsToCalculate(H);
+		    //EMEarthLocal->SetHankelTransformMethod(DIGITALFILTERING);
+		    //EMEarthLocal->SetHankelTransformMethod(FHTKEY201);
+		    EMEarthLocal->SetHankelTransformMethod(hType);
+		    //EMEarthLocal->SetHankelTransformMethod(GAUSSIANQUADRATURE);
+
+		//EMEarthLocal->AttachReceiverPoints(this->Receiver);
+		// For testing with one time only
+		//DFIntegrate->Compute(1,1,1e-16);
+		//std::cout<<DFIntegrate->GetAnswer()<<std::endl;
+		//
+		NumTimes = this->TimeGates.size();
+		//Testing
+		//std::cout << "NumTimes: " << NumTimes << std::endl;
+		this->ModelledData.resize(NumTimes,2);
+		for (int ii=0;ii<NumTimes;ii++) {
+			//TESTING!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+			//RELAXING THE VALUE!
+			DFIntegrate->Compute(this->TimeGates(ii), 1, 1e-7);
+			//Testing
+			//std::cout << "DFIntegrate done computing" << std::endl;
+			answer = DFIntegrate->GetAnswer()(0);
+			answer = (2./PI)*answer;
+			this->ModelledData(ii,0) = this->TimeGates(ii);
+			this->ModelledData(ii,1) = answer;
+			//std::cout << "   " << TimeGates(ii) << "  " <<
+			//	answer << std::endl;
+			//std::cout << "   " << this->ModelledData(ii,0) << "  " <<
+			//	this->ModelledData(ii,1) << std::endl;
+			// Call cosine transform which calls argument
+		}
+		//
+		TEMIntKern->Delete();
+		EMEarthLocal->Delete();
+		DFIntegrate->Delete();
+
+	}
+
+    void InstrumentTem::MakeLaggedCalculation(const HANKELTRANSFORMTYPE& hType) {
+
+        EMEarth1D *EMEarthLocal=EMEarth1D::New();
+		    EMEarthLocal->AttachLayeredEarthEM(this->EarthMod);
+		    EMEarthLocal->SetFieldsToCalculate(H);
+		    EMEarthLocal->SetHankelTransformMethod(hType);
+            EMEarthLocal->AttachReceiverPoints(this->Receiver);
+
+		TemIntegrationKernel *TEMIntKern=TemIntegrationKernel::New();
+
+		    TEMIntKern->SetReceiver(this->Receiver);
+		    TEMIntKern->SetEMEarth1D(EMEarthLocal);
+
+
+		if (this->Dipole != NULL) {  //AND this->Antenna == NULL
+			EMEarthLocal->AttachDipoleSource(this->Dipole);
+			TEMIntKern->SetDipole(this->Dipole);
+            Dipole->SetNumberOfFrequencies(1);
+		}
+		if (this->Antenna != NULL) { //AND this->Dipole == NULL
+			EMEarthLocal->AttachWireAntenna(this->Antenna);
+            Antenna->SetCurrent(1);
+			TEMIntKern->SetTransmitter(this->Antenna);
+            Antenna->SetNumberOfFrequencies(1);
+		}
+
+
+        // TODO IMPORTANT!!
+        // Compute number of lagged convolutions to do, TODO, need to make sure we do these
+        // TO THE LATEST time needed for multiple pulse subtraction!!!
+        int ilag = 1;
+        Real sub = 2.1*PulseT + 2.*NPreviousPulse*PulseT;
+        if (!bipolarWaveform) sub = NPreviousPulse*PulseT;
+
+        //TimeGates.array() += RefTime;
+        //RefTime = 0;
+
+        // This is a critical line, for reasons I don't understand, it's important to calculate past the
+        // theoretical GateWidths(0)/2.
+        while ( (TimeGates.tail(1)(0)+sub)*std::pow(1./exp(.1), ilag-1) > TimeGates(0)-GateWidths(0) ) ++ ilag;
+
+		//DigitalFilterSinTrans *DFIntegrate=DigitalFilterSinTrans::New(); // use with step response kernel
+		DigitalFilterCosTrans *DFIntegrate=DigitalFilterCosTrans::New();   // use with impulse response kernel
+		    DFIntegrate->AttachKernel(TEMIntKern);
+            DFIntegrate->SetNumConv(ilag);
+		    DFIntegrate->Compute( this->TimeGates.tail(1)(0)+sub, 1, 1e-7 ); // rho ntol, tol=1e-7 to 1e-13
+
+        CubicSplineInterpolator *Spline = CubicSplineInterpolator::New();
+            //Spline->SetKnots( DFIntegrate->GetAbscissaArguments().array(), (2./PI) * DFIntegrate->GetAnswer().col(0).array() );
+            Spline->SetKnots( DFIntegrate->GetAbscissaArguments().array(), (.25/PI) * DFIntegrate->GetAnswer().col(0).array() );
+
+
+		this->ModelledData.resize(TimeGates.size(), 2);
+            this->ModelledData.col(0) = TimeGates;
+            this->ModelledData.col(1).setZero();
+
+        //  This is non-extrapolated times and values
+        //this->ModelledData.resize(ilag, 2);
+        //    this->ModelledData.col(0) = DFIntegrate->GetAbscissaArguments(); // this->TimeGates(ii);
+		//	this->ModelledData.col(1) = (2./PI)*DFIntegrate->GetAnswer();
+        //std::cout <<  (2./PI)*DFIntegrate->GetAnswer().transpose()  << std::endl;
+
+        // Take into account receiver gate integration and tx waveform
+        FoldAndConvolve(Spline);
+
+        // Direct caclulation, step response to use need re reset temintegrationkernel back to step!
+		//	this->ModelledData.col(1) = (2./PI)*Spline->InterpolateOrderedSet( TimeGates );
+
+        Spline->Delete();
+	    TEMIntKern->Delete();
+		EMEarthLocal->Delete();
+		DFIntegrate->Delete();
+
+	}
+
+	// =======================  Access  =====================================
+
+	void InstrumentTem::SetPulse( const VectorXr& Amp, const VectorXr& times, bool bipolar ) {
+
+        bipolarWaveform = bipolar;
+        assert(Amp.size() == times.size());
+
+        TxAmp = Amp;
+        TxAbs = times;
+
+        TxDiff = VectorXr::Zero(TxAmp.size());
+        TxDelta = VectorXr::Zero(TxAmp.size());
+
+        for (int ip=1; ip<TxAmp.size(); ++ ip) {
+            TxDiff(ip)  = (TxAmp(ip-1)-TxAmp(ip  )) /
+                          (TxAbs(ip  )-TxAbs(ip-1)) ;
+            TxDelta(ip) = (TxAmp(ip-1)-TxAmp(ip  )) ;
+        }
+
+        /*
+        std::cout << "diff "  << TxDiff.transpose() << std::endl;
+        std::cout << "delta "  << TxDelta.transpose() << std::endl;
+        std::cout << "amp "  << TxAmp.transpose() << std::endl;
+        std::cout << "abs "  << TxAbs.transpose() << std::endl;
+        */
+	}
+
+	void InstrumentTem::EMEarthModel(LayeredEarthEM* Earth) {
+		if (this->EarthMod != NULL) {
+			this->EarthMod->DetachFrom(this);
+		}
+		//std::cout << "InstrumentTem: EarthMod null test" << std::endl;
+		Earth->AttachTo(this);
+		//std::cout << "InstrumentTem: EarthMod attached" << std::endl;
+		this->EarthMod = Earth;
+		//std::cout << "InstrumentTem: EMEarthModel Attached" << std::endl;
+
+	}
+
+	void InstrumentTem::SetTransmitLoop(WireAntenna *antennae) {
+		if (this->Antenna != NULL) {
+			this->Antenna->DetachFrom(this);
+		}
+		antennae->AttachTo(this);
+		this->Antenna = antennae;
+		if (this->Dipole != NULL) {
+			this->Dipole->DetachFrom(this);
+		}
+		//std::cout << "InstrumentTem: TransmitLoop Attached" << std::endl;
+
+	}
+
+	void InstrumentTem::SetDipoleSource(DipoleSource* dipolesource) {
+		if (this->Dipole != NULL) {
+			this->Dipole->DetachFrom(this);
+		}
+		dipolesource->AttachTo(this);
+		this->Dipole = dipolesource;
+		if (this->Antenna != NULL) {
+			this->Antenna->DetachFrom(this);
+		}
+	}
+
+	void InstrumentTem::SetReceiver(ReceiverPoints* Receivers) {
+		if (this->Receiver != NULL) {
+			this->Receiver->DetachFrom(this);
+		}
+		Receivers->AttachTo(this);
+		this->Receiver = Receivers;
+		//std::cout << "InstrumentTem: Receivers Attached" << std::endl;
+
+	}
+
+	void InstrumentTem::SetTimes(const VectorXr &times) {
+		this->TimeGates = times;
+	}
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  InstrumentTem
+    //      Method:  SetReceiverType
+    //--------------------------------------------------------------------------------------
+    void InstrumentTem::SetReceiverType ( const ReceiverType& rt ) {
+        RType = rt;
+        return ;
+    }		// -----  end of method InstrumentTem::SetReceiverType  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  InstrumentTEM
+    //      Method:  SetTimeGates
+    //--------------------------------------------------------------------------------------
+    void InstrumentTem::SetTimeGates ( const VectorXr &centres, const VectorXr& widths  ) {
+        assert (centres.size() == widths.size());
+        TimeGates = centres;
+        GateWidths = widths;
+        return ;
+    }		// -----  end of method InstrumentTEM::SetTimeGates  -----
+
+
+
+
+	int InstrumentTem::GetNumberOfTimes() {
+
+		return this->TimeGates.size();
+	}
+
+	MatrixXr InstrumentTem::GetMeasurements() {
+
+		return this->ModelledData;
+	}
+
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  InstrumentTem
+    //      Method:  SetReferenceTime
+    //--------------------------------------------------------------------------------------
+    void InstrumentTem::SetReferenceTime ( const Real& rtime ) {
+        RefTime = rtime;
+        return ;
+    }		// -----  end of method InstrumentTem::SetReferenceTime  -----
+
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  InstrumentTem
+    //      Method:  FoldAndConvolve
+    //--------------------------------------------------------------------------------------
+    void InstrumentTem::FoldAndConvolve ( CubicSplineInterpolator* Spline ) {
+
+        const static Real GLW[3] = {.5555556, .8888889, .5555556};
+        const static Real GLX[3] = {-.7745967, 0., .7745967};
+
+        // TODO BUG check against LEROI!!!
+        //SubtractPrevious(Spline);
+
+
+        switch (RType) {
+            case INDUCTIVE:
+                // Differentiate to compute impulse response for step input
+                // Iterate over time gate
+                for (int ig=0; ig<TimeGates.size(); ++ig) {
+                    this->ModelledData.col(1)[ig] =
+                                  ( ( ConvolveWaveform(Spline, RefTime + TimeGates[ig] - GateWidths[ig]/2.) -
+                                      ConvolveWaveform(Spline, RefTime + TimeGates[ig] + GateWidths[ig]/2.) ) / GateWidths[ig]);
+                }
+                break;
+
+            case MAGNETOMETER:
+                for (int ig=0; ig<TimeGates.size(); ++ig) {
+                    /*
+                    TC(2) = (TCLS(JT) + TOPN(JT)) / 2.
+                    TC(1) = TC(2) + HWIDTH * GLX(1)
+                    TC(3) = TC(2) + HWIDTH * GLX(3)
+                    */
+                    this->ModelledData.col(1)[ig] = 0;
+                    for (int ii=0; ii<3; ++ii) {
+                        //Real tt = RefTime + TimeGates[ig] + GLX[ii]*(GateWidths[ig]/2.);
+                        Real tt = RefTime + TimeGates[ig] + GLX[ii]*(GateWidths[ig]/2.);
+                        this->ModelledData.col(1)[ig] += ConvolveWaveform(Spline, tt) * GLW[ii]/2.;
+                    }
+                }
+                break;
+
+            case ELECTRIC:
+                throw std::runtime_error("InstrumentTEM->FoldAndConvolve with Electic Receivers is not implimented");
+                break;
+        }
+
+        return ;
+    }		// -----  end of method InstrumentTem::FoldAndConvolve  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  InstrumentTem
+    //      Method:  ConvolveWaveform
+    //--------------------------------------------------------------------------------------
+    Real InstrumentTem::ConvolveWaveform ( CubicSplineInterpolator* Spline, const Real& t ) {
+        static const Real T0MIN = 1e-7;
+        Real cnv(0);
+        Real tf = t - Spline->GetKnotAbscissa()[0];
+        bool der = false;
+        Real tend(0);
+        for (int ip=1; ip<TxAmp.size(); ++ip) {
+            if (TxAbs(ip) < T0MIN) continue;
+            if (TxAbs(ip-1) > tf)  break;
+
+            Real tb = t - std::min(tf, TxAbs(ip));
+            Real delt = TxAbs(ip) - TxAbs(ip-1);
+
+            der = false;
+            if (delt > T0MIN) {
+                tend = t - TxAbs(ip-1);
+                der = true;
+            }
+
+            if (der) {
+                //std::cout.precision(16);
+                // TODO Integrate seems to be kind of screwy!! Affecting early/on times
+                cnv += TxDiff(ip) * Spline->Integrate(tb, tend, 41200); //CUBINT (TRP,YPLS,NTYPLS,TB,TEND)
+                // TODO bug in direct spline integration, works sometimes
+                //cnv += TxDiff(ip) * Spline->Integrate(tb, tend);
+                //cnv += Spline->Integrate(tb, tend, 6264); //CUBINT (TRP,YPLS,NTYPLS,TB,TEND)
+                //Real temp = Spline->Integrate(tb, tend, 10036); //CUBINT (TRP,YPLS,NTYPLS,TB,TEND)
+                //Real temp2 = Spline->Integrate(tb, tend); //CUBINT (TRP,YPLS,NTYPLS,TB,TEND)
+                //std::cout << "der " << TxDiff(ip) << "\t" << std::scientific << tb << "\t" << tend << "\t" << MU0*temp2 << "\t" << MU0*temp << "\n";
+                //cnv += temp;
+            } else {
+                cnv += TxDelta(ip) * Spline->Interpolate(tb); //CUBVAL (TRP,YPLS,NTYPLS,TB)
+            }
+        }
+        return cnv;
+
+    }		// -----  end of method InstrumentTem::ConvolveWaveform  -----
+
+
+    //--------------------------------------------------------------------------------------
+    //       Class:  InstrumentTem
+    //      Method:  SubtractPrevious
+    //--------------------------------------------------------------------------------------
+    void InstrumentTem::SubtractPrevious ( CubicSplineInterpolator *Spline ) {
+        // Start by calculating impulse response of this pulse plus any arbitrary number of previous pulses at this
+        // repetition frequency
+        VectorXr aTimeGates = Spline->GetKnotAbscissa();
+        Real pol (1.);
+        if (bipolarWaveform) pol = -1.;
+        VectorXr PrevPulse = aTimeGates.array() + PulseT;
+		// TODO, if not bipolar what does convention say, is this added or should this be zero and handled only by nPreviousPulse?
+        VectorXr Fold = Spline->GetKnotOrdinate( ); // +
+        //VectorXr Fold =  pol*Spline->InterpolateOrderedSet( PrevPulse ) ;
+        VectorXr PrevPulse1; // = PrevPulse.array(); // + PulseT;
+        for (int ip=0; ip<NPreviousPulse; ++ip) {
+            PrevPulse1.array() += PrevPulse.array() + PulseT;
+            PrevPulse.array() += PrevPulse1.array() + PulseT;
+            Fold += Spline->InterpolateOrderedSet( PrevPulse1 ) + pol*Spline->InterpolateOrderedSet( PrevPulse ) ;
+        }
+        Spline->ResetKnotOrdinate(Fold);
+        return ;
+    }		// -----  end of method InstrumentTem::SubtractPrevious  -----
+
+
+
+} // namespace Lemma

Modules/TEM1D/src/inversesolvertem1d.cpp

@@ -0,0 +1,419 @@
+/* This file is part of Lemma, a geophysical modelling and inversion API */
+
+/* This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
+
+/**
+  @file
+  @author   M. Andy Kass
+  @date     03/23/2011
+  @version  $Id: inversesolvertem1d.cpp 193 2014-11-10 23:51:41Z tirons $
+ **/
+
+#include "inversesolvertem1d.h"
+
+namespace Lemma {
+
+	std::ostream &operator<<(std::ostream &stream,
+		const InverseSolverTEM1D &ob) {
+		stream << *(LemmaObject*)(&ob);
+		stream << "Wire antenna source address: " << ob.Antenna << std::endl;
+		stream << "Dipole source address: " << ob.Dipole << std::endl;
+		stream << *ob.Receiver << std::endl;
+		stream << *ob.StartingMod << std::endl;
+		stream << *ob.RecoveredMod << std::endl;
+		stream << *ob.InstrumentFor << std::endl;
+		return stream;
+	}
+
+    // ====================  LIFECYCLE     =======================
+
+	InverseSolverTEM1D::InverseSolverTEM1D(const std::string &name) :
+		InverseSolver(name),Antenna(NULL), Dipole(NULL),
+		Receiver(NULL), StartingMod(NULL), RecoveredMod(NULL),
+		InstrumentFor(NULL) {
+
+		this->InstrumentFor = InstrumentTem::New();
+		//this->SCondIndex.resize(42);
+		//this->SThickIndex.resize(42);
+		//this->SCondIndex(0) = 42;
+		//this->SThickIndex(0) = 42;
+	}
+
+	InverseSolverTEM1D::~InverseSolverTEM1D() {
+		if (NumberOfReferences !=0) throw DeleteObjectWithReferences(this);
+
+		if (this->Antenna != NULL) this->Antenna->DetachFrom(this);
+
+		if (this->Dipole != NULL) this->Dipole->DetachFrom(this);
+
+		if (this->Receiver != NULL) this->Receiver->DetachFrom(this);
+
+		if (this->StartingMod != NULL) this->StartingMod->DetachFrom(this);
+
+		if (this->RecoveredMod != NULL) this->RecoveredMod->DetachFrom(this);
+
+		this->InstrumentFor->Delete();
+
+	}
+
+    InverseSolverTEM1D* InverseSolverTEM1D::New() {
+        InverseSolverTEM1D*  Obj =
+            new InverseSolverTEM1D( "InverseSolverTEM1D" );
+        Obj->AttachTo(Obj);
+        return Obj;
+
+    }
+
+    void InverseSolverTEM1D::Delete() {
+        this->DetachFrom(this);
+    }
+
+    void InverseSolverTEM1D::Release() {
+        delete this;
+    }
+
+    // ====================  OPERATIONS    =======================
+
+	void InverseSolverTEM1D::Calculate() {
+		MatrixXr jac;
+		VectorXr newthickness;
+		VectorXcr newconductivity;
+		VectorXr oldthickness;
+		VectorXcr oldconductivity;
+		MatrixXr olddata;
+		MatrixXr newdata;
+		VectorXr deltathick;
+		VectorXcr deltacond;
+		MatrixXr H;
+		VectorXr g;
+		VectorXr p;
+		VectorXr s;
+		VectorXr y;
+
+		//int nrec=42;
+		int nlayers=42;
+
+		this->InstrumentFor->EMEarthModel(this->RecoveredMod);
+		this->InstrumentFor->SetTransmitLoop(this->Antenna);
+		this->InstrumentFor->SetReceiver(this->Receiver);
+		this->InstrumentFor->SetTimes(this->Times);
+
+		nlayers = this->RecoveredMod->GetNumberOfLayers();
+		//nrec = this->Receiver->GetNumberOfReceivers();
+		//check for parameters set
+		if (this->SCondIndex.size() == 0 /*&& SCondIndex(0) == 42*/) {
+			//std::cout << "Cond Index is null" << std::endl;
+			this->SCondIndex.resize(nlayers-1);
+			for (int ii=1;ii<nlayers;ii++) {
+				this->SCondIndex(ii-1)=ii;
+			}
+		}
+		if (this->SThickIndex.size()==0 /*&& SThickIndex(0)==42*/) {
+			//std::cout << "Thickness Index is null" << std::endl;
+			this->SThickIndex.resize(nlayers-2);
+			for (int ii=0;ii<nlayers-2;ii++) {
+				this->SThickIndex(ii)=ii+1;
+			}
+		}
+
+		std::cout << "Thickness indices to solve for: " << this->SThickIndex
+			<< std::endl;
+		//std::cout << "Conductivity indices to solve for: " << this->SCondIndex
+		//	<< std::endl;
+
+
+		//Real alpha;
+
+		// while \nabla g > \epsilon
+		// Forward model from starting
+		this->InstrumentFor->MakeLaggedCalculation(FHTKEY201);
+		olddata = this->InstrumentFor->GetMeasurements();
+		// Get A Jacobian Matrix
+		jac = this->CalcJac(this->RecoveredMod);
+
+		// Output jacobian matrix
+		std::ofstream outfile2;
+		outfile2.open("jacobian.out");
+		for (int ii=0; ii<jac.rows();ii++) {
+			for (int jj=0;jj<jac.cols();jj++) {
+				outfile2 << jac(ii,jj) << "    ";
+			}
+			outfile2 << std::endl;
+		}
+		outfile2.close();
+
+		H = jac.transpose()*jac;
+		std::cout << "H: " << std::endl;
+		std::cout << H << std::endl;
+
+		//Temporary solution for only one linear step
+		//delta m = (JTJ)^-1JTd
+		//VectorXr x0;
+		//VectorXr md;
+		//x0.resize(jac.cols());
+		//x0.setZero();
+		//VectorXr jtd;
+		//md = this->MeasuredData.col(0);
+		//std::cout << md << std::endl;
+		//jtd = jac.transpose()*md;
+		//std::cout << jtd.size() << std::endl;
+		//Real tol;
+		//int iter;
+		//tol = 1.e-8;
+		//iter = 1000;
+		//this->RecModStep = CG(H,x0,jtd,iter,tol);
+		//std::cout << this->RecModStep << std::endl;
+
+		// Gauss-Newton Solution
+		//
+
+
+		// Quasi newton solution
+		// while ||\nabla g|| > \epsilon
+			// g = jac.transpose()*(olddata(:,1)-this->MeasuredData(:,1));
+			// p = H*g*(-1);
+			// newmod = oldmod + alpha * p
+			// s = alpha * p
+			// y = g(k+1) - g(k)
+			// H(k+1) = H - (H*s*s.transpose()*H)/(s.T*H*s) + (y*y.T)/(y.T*s)
+		// Solve for model perturbation
+		// end while
+
+
+	}
+
+	MatrixXr InverseSolverTEM1D::CalcJac(LayeredEarthEM* m0) {
+		MatrixXr jac;
+		int nrec;
+		int nlayers;
+		int nparams;
+		int nfsigs;
+		//int nflays;
+		Real step = 0.05;
+		VectorXr currentsigma;
+		VectorXr currentthick;
+		VectorXr newsigma;
+		VectorXr newthick;
+		Complex ctemp;
+		VectorXcr vctemp;
+		VectorXr params;
+		MatrixXr currentmeasurements;
+		MatrixXr perturbedmeasurements;
+		MatrixXr diffs;
+
+		nrec = this->Receiver->GetNumberOfReceivers();
+		nlayers = this->StartingMod->GetNumberOfLayers();
+		nfsigs = this->SCondIndex.size();
+		//nflays = this->SThickIndex.size();
+		nparams = this->SCondIndex.size() + this->SThickIndex.size();
+		jac.resize(nrec*this->Times.size(),nparams); /// TODO memory leak
+		params.resize(nparams);
+		std::cout << this->SThickIndex << std::endl;
+
+		//Need to set currentsigma and currentthick
+		//
+		currentsigma.resize(nlayers);
+		currentthick.resize(nlayers);
+		currentsigma = m0->GetLayerConductivity().array().real();
+		for (int ii=0;ii<nlayers;ii++) {
+			currentthick(ii) = m0->GetLayerThickness(ii);
+		}
+		newsigma = currentsigma;
+		newthick = currentthick;
+
+		currentmeasurements = this->InstrumentFor->GetMeasurements();
+
+		// Concatenate thicknesses and conductivities into one vector (params)
+		// Here is where I write over the original parameters
+		for (int ii=0;ii<SCondIndex.size();ii++) {
+			params(ii)=currentsigma(this->SCondIndex(ii));
+		}
+		int jj = 0;
+		for (int ii=SCondIndex.size();ii<nparams;ii++) {
+			params(ii) = currentthick(this->SThickIndex(jj)); //this was +1
+			jj++;
+		}
+		std::cout << "Size Params: " << params.size() << std::endl;
+		std::cout << "Size newsigma: " << newsigma.size() << std::endl;
+		std::cout << "Size newthick: " << newthick.size() << std::endl;
+		std::cout << "Size currentsigma: " << currentsigma.size() << std::endl;
+		std::cout << "Size currentthick: " << currentthick.size() << std::endl;
+		std::cout << "Thickness vector : " << currentthick << std::endl;
+		std::cout << "Sigma vector: " << currentsigma << std::endl;
+
+
+
+		//std::cout << "Jacobian size: " << jac.rows() << " x " <<
+		//	jac.cols() << std::endl;
+
+		Real tparam;
+		for (int jj=0;jj<nparams;jj++) {
+			tparam = params(jj)*step;
+			params(jj) = params(jj) + tparam;
+			newsigma = currentsigma;
+			newthick = currentthick;
+			std::cout << "New sigma, in loop: " << newsigma << std::endl;
+			std::cout << "New thick, in loop: " << newthick << std::endl;
+			//plop params back into newsigma and newthick
+			for (int kk=0;kk<nfsigs;kk++) {
+				std::cout << "Sigma index: " << this->SCondIndex(kk) << std::endl;
+				newsigma(this->SCondIndex(kk)) = params(kk);
+			}
+			int ii = 0;
+			std::cout << "Params, in loop: " << params << std::endl;
+			for (int kk=nfsigs;kk<nparams;kk++) {
+				std::cout << "Thick index: " << this->SThickIndex(ii) << std::endl;
+				newthick(this->SThickIndex(ii)) = params(kk); //here is the problem
+				//params is loaded incorrectly
+				ii++;
+			}
+			std::cout << "New thickness: " << newthick << std::endl;
+			std::cout << "New cond: " << newsigma << std::endl;
+			m0->SetLayerThickness(newthick.segment(1,newthick.size()-2));
+			m0->SetLayerConductivity(newsigma.cast<Complex>());
+			std::cout << *m0 << std::endl;
+
+			this->InstrumentFor->MakeLaggedCalculation(FHTKEY201);
+			perturbedmeasurements = this->InstrumentFor->GetMeasurements();
+			diffs = currentmeasurements - perturbedmeasurements;
+			diffs = diffs / tparam;
+			//Put the values back
+			params(jj) = params(jj) - tparam;
+			for (int ii=0;ii<jac.rows();ii++) {
+				jac(ii,jj)=diffs(ii,1);
+			}
+			std::cout << "Current Jacobian: " << std::endl;
+			std::cout << jac << std::endl;
+
+		}
+
+		return jac;
+
+	}
+
+	void InverseSolverTEM1D::AttachStartMod(LayeredEarthEM* inpstartmod) {
+		if (this->StartingMod != NULL) {
+			this->StartingMod->DetachFrom(this);
+		}
+		inpstartmod->AttachTo(this);
+		this->StartingMod = inpstartmod;
+	}
+
+	void InverseSolverTEM1D::AttachRecMod(LayeredEarthEM* inprecmod) {
+		if (this->RecoveredMod != NULL) {
+			this->RecoveredMod->DetachFrom(this);
+		}
+		inprecmod->AttachTo(this);
+		this->RecoveredMod = inprecmod;
+	}
+
+	void InverseSolverTEM1D::AttachWireAntenna(WireAntenna* inpwireantenna) {
+		if (this->Antenna != NULL) {
+			this->Antenna->DetachFrom(this);
+		}
+		inpwireantenna->AttachTo(this);
+		this->Antenna = inpwireantenna;
+	}
+
+	void InverseSolverTEM1D::AttachDipoleSource(DipoleSource* inpdipsource) {
+		if (this->Dipole != NULL) {
+			this->Dipole->DetachFrom(this);
+		}
+		inpdipsource->AttachTo(this);
+		this->Dipole = inpdipsource;
+	}
+
+	void InverseSolverTEM1D::AttachReceiver(ReceiverPoints* inpreceiver) {
+		if (this->Receiver != NULL) {
+			this->Receiver->DetachFrom(this);
+		}
+		inpreceiver->AttachTo(this);
+		this->Receiver = inpreceiver;
+	}
+
+	void InverseSolverTEM1D::SetTimes(VectorXr &inptimes) {
+		this->Times = inptimes;
+
+	}
+
+	void InverseSolverTEM1D::ShowSoln() {
+		int ntimes;
+		ntimes = this->InstrumentFor->GetNumberOfTimes();
+
+		for (int ii=0;ii<ntimes;ii++) {
+			std::cout<<"  "<<this->InstrumentFor->GetMeasurements()(ii,0)
+			<<"  "<<this->InstrumentFor->GetMeasurements()(ii,1)<<std::endl;
+		}
+	}
+
+	void InverseSolverTEM1D::WriteSoln(const std::string &filename) {
+		int nlayers;
+		VectorXcr conductivities;
+		VectorXr thicknesses;
+
+		nlayers = this->RecoveredMod->GetNumberOfLayers();
+		conductivities.resize(nlayers);
+		thicknesses.resize(nlayers);
+		conductivities = this->RecoveredMod->GetLayerConductivity();
+		for (int ii=0;ii<nlayers;ii++) {
+			thicknesses(ii) = this->RecoveredMod->GetLayerThickness(ii);
+		}
+
+		std::ofstream outfile1;
+		outfile1.open(filename.c_str());
+		// Model file has format:
+		// thickness (m) 	conductivity (S/m)
+		for (int ii=0;ii<nlayers;ii++) {
+			outfile1 << thicknesses(ii) << "    " << conductivities(ii) <<
+				"    " << std::endl;
+		}
+		outfile1.close();
+
+	}
+
+	void InverseSolverTEM1D::SetFreeParams(const VectorXi &layers,
+		const VectorXi &cond) {
+
+		this->SCondIndex = cond;
+		this->SThickIndex = layers;
+	}
+
+	void InverseSolverTEM1D::AttachMeasuredData(const MatrixXr &data) {
+		this->MeasuredData = data;
+
+	}
+
+	int InverseSolverTEM1D::NumberOfIterations() {
+
+		return 42;
+	}
+
+	bool InverseSolverTEM1D::Success() {
+
+		return false;
+	}
+
+	VectorXr InverseSolverTEM1D::GetPhiMVector() {
+		VectorXr temp;
+		temp.resize(1);
+
+		temp(0)=42;
+		return temp;
+	}
+
+	VectorXr InverseSolverTEM1D::GetPhiDVector() {
+		VectorXr temp;
+		temp.resize(1);
+		temp(0) = 42;
+		return temp;
+	}
+
+	void InverseSolverTEM1D::FillInG(const Vector3r& pos,
+		const Vector3r& step) {
+
+	}
+
+}
+